Re: you are making it far too difficult

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Re: you are making it far too difficult

Spencer Brackett
Thank you for the help! I tried using the read.table command in my RStudio
using the following argument, and managed to open the file.

GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)

However, my data did not unpack as yours did. I again only received a table
of true and flase distinctions per column, and my environment tab says that
there is 0 observations upon 0 variables.

I believe I should be getting data similar to what you got, as it would
appear that your’s actually contains relevant gene/protein expression info.

On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
[hidden email]> wrote:

> Once you have your TSV files just use something as
>
> x = read.table('protein_expression.tsv', h = T, sep = '\t')
>
> Do not copy paste the code of this email because it is formatted and would
> not work in R.
>
>
> Best
>
> F
>
> PS the data looks like this to me
>
> head(x)
>   icgc_donor_id project_code icgc_specimen_id icgc_sample_id
>  submitted_sample_id analysis_id        antibody_id gene_name
> 1       DO12370       GBM-US          SP26475       SA131594
> TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
> 2       DO12370       GBM-US          SP26475       SA131594
> TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
> 3       DO12370       GBM-US          SP26475       SA131594
> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
> 4       DO12370       GBM-US          SP26475       SA131594
> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
> 5       DO12370       GBM-US          SP26475       SA131594
> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
> 6       DO12370       GBM-US          SP26475       SA131594
> TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
>   gene_stable_id gene_build_version normalized_expression_level
> verification_status verification_platform
> 1             NA                 NA                  -1.1636330
> not tested                    NA
> 2             NA                 NA                  -1.7969721
> not tested                    NA
> 3             NA                 NA                  -0.7256390
> not tested                    NA
> 4             NA                 NA                   0.6498421
> not tested                    NA
> 5             NA                 NA                  -1.0262844
> not tested                    NA
> 6             NA                 NA                   1.5186400
> not tested                    NA
>                                         platform
> 1 M.D. Anderson Reverse Phase Protein Array Core
> 2 M.D. Anderson Reverse Phase Protein Array Core
> 3 M.D. Anderson Reverse Phase Protein Array Core
> 4 M.D. Anderson Reverse Phase Protein Array Core
> 5 M.D. Anderson Reverse Phase Protein Array Core
> 6 M.D. Anderson Reverse Phase Protein Array Core
>
>
>
> experimental_protocol
> 1 MDA_RPPA_Core
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> 2 MDA_RPPA_Core
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> 3 MDA_RPPA_Core
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> 4 MDA_RPPA_Core
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> 5 MDA_RPPA_Core
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> 6 MDA_RPPA_Core
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>   raw_data_repository          raw_data_accession
> 1                TCGA TCGA-19-5960-01A-13-1900-20
> 2                TCGA TCGA-19-5960-01A-13-1900-20
> 3                TCGA TCGA-19-5960-01A-13-1900-20
> 4                TCGA TCGA-19-5960-01A-13-1900-20
> 5                TCGA TCGA-19-5960-01A-13-1900-20
> 6                TCGA TCGA-19-5960-01A-13-1900-20
>
> --
> Federico Calboli
> LBEG - Laboratory of Biodiversity and Evolutionary Genomics
> Charles Deberiotstraat 32
> <https://maps.google.com/?q=Charles+Deberiotstraat+32&entry=gmail&source=g>
> box 2439
> 3000 Leuven
> +32 16 32 87 67
>
>
>
>
>
>

        [[alternative HTML version deleted]]

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Re: you are making it far too difficult

Spencer Brackett
Mr. Calboli,

After beginning to unpack the GBM file you sent me via directly importing
it unit my console, I received the following:

View(GBM_PEXP.tsv)

**Note that I named the file GBM_PEXP.tsv)**

  Upon downloading, my script now contains a 2 by 2 table, with the x
column still containing encoded script. As for my Data summary to the
 right, this new file reports that 2 objects are acting upon 1 variable.
How should I proceed?

-Spencer

On Thu, Dec 27, 2018 at 3:12 PM Federico Calboli <
[hidden email]> wrote:

> Unpack these files.
>
> F
>
>

        [[alternative HTML version deleted]]

______________________________________________
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Re: you are making it far too difficult

Sarah Goslee
In reply to this post by Spencer Brackett
On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
<[hidden email]> wrote:
>
> Thank you for the help! I tried using the read.table command in my RStudio
> using the following argument, and managed to open the file.
>
> GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)

Note that sep="/t" is NOT the same thing as the sep="\t" you were
advised to use.




>
> However, my data did not unpack as yours did. I again only received a table
> of true and flase distinctions per column, and my environment tab says that
> there is 0 observations upon 0 variables.
>
> I believe I should be getting data similar to what you got, as it would
> appear that your’s actually contains relevant gene/protein expression info.
>
> On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
> [hidden email]> wrote:
>
> > Once you have your TSV files just use something as
> >
> > x = read.table('protein_expression.tsv', h = T, sep = '\t')
> >
> > Do not copy paste the code of this email because it is formatted and would
> > not work in R.
> >
> >
> > Best
> >
> > F
> >
> > PS the data looks like this to me
> >
> > head(x)
> >   icgc_donor_id project_code icgc_specimen_id icgc_sample_id
> >  submitted_sample_id analysis_id        antibody_id gene_name
> > 1       DO12370       GBM-US          SP26475       SA131594
> > TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
> > 2       DO12370       GBM-US          SP26475       SA131594
> > TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
> > 3       DO12370       GBM-US          SP26475       SA131594
> > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
> > 4       DO12370       GBM-US          SP26475       SA131594
> > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
> > 5       DO12370       GBM-US          SP26475       SA131594
> > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
> > 6       DO12370       GBM-US          SP26475       SA131594
> > TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
> >   gene_stable_id gene_build_version normalized_expression_level
> > verification_status verification_platform
> > 1             NA                 NA                  -1.1636330
> > not tested                    NA
> > 2             NA                 NA                  -1.7969721
> > not tested                    NA
> > 3             NA                 NA                  -0.7256390
> > not tested                    NA
> > 4             NA                 NA                   0.6498421
> > not tested                    NA
> > 5             NA                 NA                  -1.0262844
> > not tested                    NA
> > 6             NA                 NA                   1.5186400
> > not tested                    NA
> >                                         platform
> > 1 M.D. Anderson Reverse Phase Protein Array Core
> > 2 M.D. Anderson Reverse Phase Protein Array Core
> > 3 M.D. Anderson Reverse Phase Protein Array Core
> > 4 M.D. Anderson Reverse Phase Protein Array Core
> > 5 M.D. Anderson Reverse Phase Protein Array Core
> > 6 M.D. Anderson Reverse Phase Protein Array Core
> >
> >
> >
> > experimental_protocol
> > 1 MDA_RPPA_Core
> > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > 2 MDA_RPPA_Core
> > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > 3 MDA_RPPA_Core
> > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > 4 MDA_RPPA_Core
> > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > 5 MDA_RPPA_Core
> > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > 6 MDA_RPPA_Core
> > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >   raw_data_repository          raw_data_accession
> > 1                TCGA TCGA-19-5960-01A-13-1900-20
> > 2                TCGA TCGA-19-5960-01A-13-1900-20
> > 3                TCGA TCGA-19-5960-01A-13-1900-20
> > 4                TCGA TCGA-19-5960-01A-13-1900-20
> > 5                TCGA TCGA-19-5960-01A-13-1900-20
> > 6                TCGA TCGA-19-5960-01A-13-1900-20
> >


--
Sarah Goslee (she/her)
http://www.numberwright.com

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Re: you are making it far too difficult

Richard M. Heiberger
In reply to this post by Spencer Brackett
I downloaded the Donors dataset

https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D

by clicking "Export table as TSV".

Then I read it with

donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv")

Here is the transcript.

> donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv")
> donors
   Donor.ID Project.Code Primary.Site Gender Age.at.Diagnosis
1   DO10892       GBM-US        Brain Female               45
2   DO12328       GBM-US        Brain   Male               56
3   DO11657       GBM-US        Brain Female               73
4   DO13510       GBM-US        Brain Female               63
5   DO12670       GBM-US        Brain Female               63
6   DO11501       GBM-US        Brain Female               59
7   DO13809       GBM-US        Brain Female               74
8   DO13647       GBM-US        Brain   Male               56
9   DO11645       GBM-US        Brain   Male               73
10  DO14145       GBM-US        Brain Female               85
   Tumor.Stage.at.Diagnosis Survival.Time..days.  SSM CNSM  STSM   SGV
METH.A
1                        NA                   NA True True False False
 True
2                        NA                  154 True True False False
 True
3                        NA                   NA True True False False
 True
4                        NA                 1448 True True False False
 True
5                        NA                  772 True True False False
 True
6                        NA                   NA True True False False
 True
7                        NA                  213 True True False False
 True
8                        NA                  383 True True False False
 True
9                        NA                  113 True True False False
 True
10                       NA                   94 True True False False
 True
   METH.S EXP.A EXP.S PEXP miRNA.S   JCN Mutations Mutated.Genes
1   False  True  True True   False False       269           392
2   False  True False True   False False       192           263
3   False  True False True   False False       128           209
4   False  True  True True   False False       130           199
5   False  True  True True   False False       142           194
6   False  True  True True   False False       129           190
7   False  True False True   False False       130           178
8   False  True False True   False False       116           175
9   False  True False True   False False       125           174
10  False  True  True True   False False       108           169
>

I don't know how to get the download of the whole file.  It looks like you
could page through it with the page menu at the bottom of the webpage.  If
you do that, set it for 50 at a time instead of the default 10.

For the Genes and the two types of Mutation files, it will be more nuisance
this way because there are about 10000 rows for each of those three files,
thus about 200 of these statements per dataset.

I think it is time to move to the bioconductor list for specific guidance
on this type of dataset.


On Thu, Dec 27, 2018 at 3:28 PM Spencer Brackett <
[hidden email]> wrote:

> Mr. Calboli,
>
> After beginning to unpack the GBM file you sent me via directly importing
> it unit my console, I received the following:
>
> View(GBM_PEXP.tsv)
>
> **Note that I named the file GBM_PEXP.tsv)**
>
>   Upon downloading, my script now contains a 2 by 2 table, with the x
> column still containing encoded script. As for my Data summary to the
>  right, this new file reports that 2 objects are acting upon 1 variable.
> How should I proceed?
>
> -Spencer
>
> On Thu, Dec 27, 2018 at 3:12 PM Federico Calboli <
> [hidden email]> wrote:
>
> > Unpack these files.
> >
> > F
> >
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
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Re: you are making it far too difficult

Spencer Brackett
In reply to this post by Sarah Goslee
What is the significance of using / or \ ?

On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <[hidden email]> wrote:

> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
> <[hidden email]> wrote:
> >
> > Thank you for the help! I tried using the read.table command in my
> RStudio
> > using the following argument, and managed to open the file.
> >
> > GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)
>
> Note that sep="/t" is NOT the same thing as the sep="\t" you were
> advised to use.
>
>
>
>
> >
> > However, my data did not unpack as yours did. I again only received a
> table
> > of true and flase distinctions per column, and my environment tab says
> that
> > there is 0 observations upon 0 variables.
> >
> > I believe I should be getting data similar to what you got, as it would
> > appear that your’s actually contains relevant gene/protein expression
> info.
> >
> > On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
> > [hidden email]> wrote:
> >
> > > Once you have your TSV files just use something as
> > >
> > > x = read.table('protein_expression.tsv', h = T, sep = '\t')
> > >
> > > Do not copy paste the code of this email because it is formatted and
> would
> > > not work in R.
> > >
> > >
> > > Best
> > >
> > > F
> > >
> > > PS the data looks like this to me
> > >
> > > head(x)
> > >   icgc_donor_id project_code icgc_specimen_id icgc_sample_id
> > >  submitted_sample_id analysis_id        antibody_id gene_name
> > > 1       DO12370       GBM-US          SP26475       SA131594
> > > TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
> > > 2       DO12370       GBM-US          SP26475       SA131594
> > > TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
> > > 3       DO12370       GBM-US          SP26475       SA131594
> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
> > > 4       DO12370       GBM-US          SP26475       SA131594
> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
> > > 5       DO12370       GBM-US          SP26475       SA131594
> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
> > > 6       DO12370       GBM-US          SP26475       SA131594
> > > TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
> > >   gene_stable_id gene_build_version normalized_expression_level
> > > verification_status verification_platform
> > > 1             NA                 NA                  -1.1636330
> > > not tested                    NA
> > > 2             NA                 NA                  -1.7969721
> > > not tested                    NA
> > > 3             NA                 NA                  -0.7256390
> > > not tested                    NA
> > > 4             NA                 NA                   0.6498421
> > > not tested                    NA
> > > 5             NA                 NA                  -1.0262844
> > > not tested                    NA
> > > 6             NA                 NA                   1.5186400
> > > not tested                    NA
> > >                                         platform
> > > 1 M.D. Anderson Reverse Phase Protein Array Core
> > > 2 M.D. Anderson Reverse Phase Protein Array Core
> > > 3 M.D. Anderson Reverse Phase Protein Array Core
> > > 4 M.D. Anderson Reverse Phase Protein Array Core
> > > 5 M.D. Anderson Reverse Phase Protein Array Core
> > > 6 M.D. Anderson Reverse Phase Protein Array Core
> > >
> > >
> > >
> > > experimental_protocol
> > > 1 MDA_RPPA_Core
> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > > 2 MDA_RPPA_Core
> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > > 3 MDA_RPPA_Core
> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > > 4 MDA_RPPA_Core
> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > > 5 MDA_RPPA_Core
> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > > 6 MDA_RPPA_Core
> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> > >   raw_data_repository          raw_data_accession
> > > 1                TCGA TCGA-19-5960-01A-13-1900-20
> > > 2                TCGA TCGA-19-5960-01A-13-1900-20
> > > 3                TCGA TCGA-19-5960-01A-13-1900-20
> > > 4                TCGA TCGA-19-5960-01A-13-1900-20
> > > 5                TCGA TCGA-19-5960-01A-13-1900-20
> > > 6                TCGA TCGA-19-5960-01A-13-1900-20
> > >
>
>
> --
> Sarah Goslee (she/her)
> http://www.numberwright.com
>

        [[alternative HTML version deleted]]

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Re: you are making it far too difficult

Caitlin Gibbons
“\t” is an escape sequence which signifies one tab character. “/t” is NOT an escape sequence, and to R, looks like a very brief file path.

Sent from my iPhone

> On Dec 27, 2018, at 2:09 PM, Spencer Brackett <[hidden email]> wrote:
>
> What is the significance of using / or \ ?
>
>> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <[hidden email]> wrote:
>>
>> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
>> <[hidden email]> wrote:
>>>
>>> Thank you for the help! I tried using the read.table command in my
>> RStudio
>>> using the following argument, and managed to open the file.
>>>
>>> GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)
>>
>> Note that sep="/t" is NOT the same thing as the sep="\t" you were
>> advised to use.
>>
>>
>>
>>
>>>
>>> However, my data did not unpack as yours did. I again only received a
>> table
>>> of true and flase distinctions per column, and my environment tab says
>> that
>>> there is 0 observations upon 0 variables.
>>>
>>> I believe I should be getting data similar to what you got, as it would
>>> appear that your’s actually contains relevant gene/protein expression
>> info.
>>>
>>> On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
>>> [hidden email]> wrote:
>>>
>>>> Once you have your TSV files just use something as
>>>>
>>>> x = read.table('protein_expression.tsv', h = T, sep = '\t')
>>>>
>>>> Do not copy paste the code of this email because it is formatted and
>> would
>>>> not work in R.
>>>>
>>>>
>>>> Best
>>>>
>>>> F
>>>>
>>>> PS the data looks like this to me
>>>>
>>>> head(x)
>>>>  icgc_donor_id project_code icgc_specimen_id icgc_sample_id
>>>> submitted_sample_id analysis_id        antibody_id gene_name
>>>> 1       DO12370       GBM-US          SP26475       SA131594
>>>> TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
>>>> 2       DO12370       GBM-US          SP26475       SA131594
>>>> TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
>>>> 3       DO12370       GBM-US          SP26475       SA131594
>>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
>>>> 4       DO12370       GBM-US          SP26475       SA131594
>>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
>>>> 5       DO12370       GBM-US          SP26475       SA131594
>>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
>>>> 6       DO12370       GBM-US          SP26475       SA131594
>>>> TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
>>>>  gene_stable_id gene_build_version normalized_expression_level
>>>> verification_status verification_platform
>>>> 1             NA                 NA                  -1.1636330
>>>> not tested                    NA
>>>> 2             NA                 NA                  -1.7969721
>>>> not tested                    NA
>>>> 3             NA                 NA                  -0.7256390
>>>> not tested                    NA
>>>> 4             NA                 NA                   0.6498421
>>>> not tested                    NA
>>>> 5             NA                 NA                  -1.0262844
>>>> not tested                    NA
>>>> 6             NA                 NA                   1.5186400
>>>> not tested                    NA
>>>>                                        platform
>>>> 1 M.D. Anderson Reverse Phase Protein Array Core
>>>> 2 M.D. Anderson Reverse Phase Protein Array Core
>>>> 3 M.D. Anderson Reverse Phase Protein Array Core
>>>> 4 M.D. Anderson Reverse Phase Protein Array Core
>>>> 5 M.D. Anderson Reverse Phase Protein Array Core
>>>> 6 M.D. Anderson Reverse Phase Protein Array Core
>>>>
>>>>
>>>>
>>>> experimental_protocol
>>>> 1 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 2 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 3 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 4 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 5 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 6 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>>  raw_data_repository          raw_data_accession
>>>> 1                TCGA TCGA-19-5960-01A-13-1900-20
>>>> 2                TCGA TCGA-19-5960-01A-13-1900-20
>>>> 3                TCGA TCGA-19-5960-01A-13-1900-20
>>>> 4                TCGA TCGA-19-5960-01A-13-1900-20
>>>> 5                TCGA TCGA-19-5960-01A-13-1900-20
>>>> 6                TCGA TCGA-19-5960-01A-13-1900-20
>>>>
>>
>>
>> --
>> Sarah Goslee (she/her)
>> http://www.numberwright.com
>>
>
>    [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: you are making it far too difficult

Spencer Brackett
In reply to this post by Richard M. Heiberger
Mr. Heiberger,

  I followed your argument and it works. I received the same data. And yes,
ICGC breakes their datasets into separate files based on data type. Thank
you for the pointer on selecting all 50 rows, as I assumed that the
entirety of gene expression data within the data set would be downloaded
through the process you followed, as it does when directly downloading the
file via a tsv.gz download.

On Thu, Dec 27, 2018 at 4:05 PM Richard M. Heiberger <[hidden email]> wrote:

> I downloaded the Donors dataset
>
>
> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D
>
> by clicking "Export table as TSV".
>
> Then I read it with
>
> donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv")
>
> Here is the transcript.
>
> > donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv")
> > donors
>    Donor.ID Project.Code Primary.Site Gender Age.at.Diagnosis
> 1   DO10892       GBM-US        Brain Female               45
> 2   DO12328       GBM-US        Brain   Male               56
> 3   DO11657       GBM-US        Brain Female               73
> 4   DO13510       GBM-US        Brain Female               63
> 5   DO12670       GBM-US        Brain Female               63
> 6   DO11501       GBM-US        Brain Female               59
> 7   DO13809       GBM-US        Brain Female               74
> 8   DO13647       GBM-US        Brain   Male               56
> 9   DO11645       GBM-US        Brain   Male               73
> 10  DO14145       GBM-US        Brain Female               85
>    Tumor.Stage.at.Diagnosis Survival.Time..days.  SSM CNSM  STSM   SGV
> METH.A
> 1                        NA                   NA True True False False
>  True
> 2                        NA                  154 True True False False
>  True
> 3                        NA                   NA True True False False
>  True
> 4                        NA                 1448 True True False False
>  True
> 5                        NA                  772 True True False False
>  True
> 6                        NA                   NA True True False False
>  True
> 7                        NA                  213 True True False False
>  True
> 8                        NA                  383 True True False False
>  True
> 9                        NA                  113 True True False False
>  True
> 10                       NA                   94 True True False False
>  True
>    METH.S EXP.A EXP.S PEXP miRNA.S   JCN Mutations Mutated.Genes
> 1   False  True  True True   False False       269           392
> 2   False  True False True   False False       192           263
> 3   False  True False True   False False       128           209
> 4   False  True  True True   False False       130           199
> 5   False  True  True True   False False       142           194
> 6   False  True  True True   False False       129           190
> 7   False  True False True   False False       130           178
> 8   False  True False True   False False       116           175
> 9   False  True False True   False False       125           174
> 10  False  True  True True   False False       108           169
> >
>
> I don't know how to get the download of the whole file.  It looks like you
> could page through it with the page menu at the bottom of the webpage.  If
> you do that, set it for 50 at a time instead of the default 10.
>
> For the Genes and the two types of Mutation files, it will be more
> nuisance this way because there are about 10000 rows for each of those
> three files, thus about 200 of these statements per dataset.
>
> I think it is time to move to the bioconductor list for specific guidance
> on this type of dataset.
>
>
> On Thu, Dec 27, 2018 at 3:28 PM Spencer Brackett <
> [hidden email]> wrote:
>
>> Mr. Calboli,
>>
>> After beginning to unpack the GBM file you sent me via directly importing
>> it unit my console, I received the following:
>>
>> View(GBM_PEXP.tsv)
>>
>> **Note that I named the file GBM_PEXP.tsv)**
>>
>>   Upon downloading, my script now contains a 2 by 2 table, with the x
>> column still containing encoded script. As for my Data summary to the
>>  right, this new file reports that 2 objects are acting upon 1 variable.
>> How should I proceed?
>>
>> -Spencer
>>
>> On Thu, Dec 27, 2018 at 3:12 PM Federico Calboli <
>> [hidden email]> wrote:
>>
>> > Unpack these files.
>> >
>> > F
>> >
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>

        [[alternative HTML version deleted]]

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Re: you are making it far too difficult

Spencer Brackett
In reply to this post by Caitlin Gibbons
So I should use “\t” proceeding on?

On Thu, Dec 27, 2018 at 4:30 PM Caitlin Gibbons <[hidden email]>
wrote:

> “\t” is an escape sequence which signifies one tab character. “/t” is NOT
> an escape sequence, and to R, looks like a very brief file path.
>
> Sent from my iPhone
>
> > On Dec 27, 2018, at 2:09 PM, Spencer Brackett <
> [hidden email]> wrote:
> >
> > What is the significance of using / or \ ?
> >
> >> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <[hidden email]>
> wrote:
> >>
> >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
> >> <[hidden email]> wrote:
> >>>
> >>> Thank you for the help! I tried using the read.table command in my
> >> RStudio
> >>> using the following argument, and managed to open the file.
> >>>
> >>> GBM_protein_expression<-read.table(file.choose(), header=TRUE,
> sep=“/t”)
> >>
> >> Note that sep="/t" is NOT the same thing as the sep="\t" you were
> >> advised to use.
> >>
> >>
> >>
> >>
> >>>
> >>> However, my data did not unpack as yours did. I again only received a
> >> table
> >>> of true and flase distinctions per column, and my environment tab says
> >> that
> >>> there is 0 observations upon 0 variables.
> >>>
> >>> I believe I should be getting data similar to what you got, as it would
> >>> appear that your’s actually contains relevant gene/protein expression
> >> info.
> >>>
> >>> On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
> >>> [hidden email]> wrote:
> >>>
> >>>> Once you have your TSV files just use something as
> >>>>
> >>>> x = read.table('protein_expression.tsv', h = T, sep = '\t')
> >>>>
> >>>> Do not copy paste the code of this email because it is formatted and
> >> would
> >>>> not work in R.
> >>>>
> >>>>
> >>>> Best
> >>>>
> >>>> F
> >>>>
> >>>> PS the data looks like this to me
> >>>>
> >>>> head(x)
> >>>>  icgc_donor_id project_code icgc_specimen_id icgc_sample_id
> >>>> submitted_sample_id analysis_id        antibody_id gene_name
> >>>> 1       DO12370       GBM-US          SP26475       SA131594
> >>>> TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
> >>>> 2       DO12370       GBM-US          SP26475       SA131594
> >>>> TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
> >>>> 3       DO12370       GBM-US          SP26475       SA131594
> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
> >>>> 4       DO12370       GBM-US          SP26475       SA131594
> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
> >>>> 5       DO12370       GBM-US          SP26475       SA131594
> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
> >>>> 6       DO12370       GBM-US          SP26475       SA131594
> >>>> TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
> >>>>  gene_stable_id gene_build_version normalized_expression_level
> >>>> verification_status verification_platform
> >>>> 1             NA                 NA                  -1.1636330
> >>>> not tested                    NA
> >>>> 2             NA                 NA                  -1.7969721
> >>>> not tested                    NA
> >>>> 3             NA                 NA                  -0.7256390
> >>>> not tested                    NA
> >>>> 4             NA                 NA                   0.6498421
> >>>> not tested                    NA
> >>>> 5             NA                 NA                  -1.0262844
> >>>> not tested                    NA
> >>>> 6             NA                 NA                   1.5186400
> >>>> not tested                    NA
> >>>>                                        platform
> >>>> 1 M.D. Anderson Reverse Phase Protein Array Core
> >>>> 2 M.D. Anderson Reverse Phase Protein Array Core
> >>>> 3 M.D. Anderson Reverse Phase Protein Array Core
> >>>> 4 M.D. Anderson Reverse Phase Protein Array Core
> >>>> 5 M.D. Anderson Reverse Phase Protein Array Core
> >>>> 6 M.D. Anderson Reverse Phase Protein Array Core
> >>>>
> >>>>
> >>>>
> >>>> experimental_protocol
> >>>> 1 MDA_RPPA_Core
> >>>>
> >>
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >>>> 2 MDA_RPPA_Core
> >>>>
> >>
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >>>> 3 MDA_RPPA_Core
> >>>>
> >>
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >>>> 4 MDA_RPPA_Core
> >>>>
> >>
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >>>> 5 MDA_RPPA_Core
> >>>>
> >>
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >>>> 6 MDA_RPPA_Core
> >>>>
> >>
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >>>>  raw_data_repository          raw_data_accession
> >>>> 1                TCGA TCGA-19-5960-01A-13-1900-20
> >>>> 2                TCGA TCGA-19-5960-01A-13-1900-20
> >>>> 3                TCGA TCGA-19-5960-01A-13-1900-20
> >>>> 4                TCGA TCGA-19-5960-01A-13-1900-20
> >>>> 5                TCGA TCGA-19-5960-01A-13-1900-20
> >>>> 6                TCGA TCGA-19-5960-01A-13-1900-20
> >>>>
> >>
> >>
> >> --
> >> Sarah Goslee (she/her)
> >> http://www.numberwright.com
> >>
> >
> >    [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: you are making it far too difficult

Sarah Goslee
In reply to this post by Spencer Brackett
\t is the symbol for a tab.
/t is two characters just as it seems. It's highly unlikely your file
is delimited with /t, which would look like
1/t2/t3

The help for read.table mentions this tangentially as part of
read.delim(), and you can find out more under ?regex - see the section
about escaping non-metacharacters with a backslash.

Sarah

On Thu, Dec 27, 2018 at 4:09 PM Spencer Brackett
<[hidden email]> wrote:

>
> What is the significance of using / or \ ?
>
> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <[hidden email]> wrote:
>>
>> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
>> <[hidden email]> wrote:
>> >
>> > Thank you for the help! I tried using the read.table command in my RStudio
>> > using the following argument, and managed to open the file.
>> >
>> > GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)
>>
>> Note that sep="/t" is NOT the same thing as the sep="\t" you were
>> advised to use.
>>
>>
>>
>>
>> >
>> > However, my data did not unpack as yours did. I again only received a table
>> > of true and flase distinctions per column, and my environment tab says that
>> > there is 0 observations upon 0 variables.
>> >
>> > I believe I should be getting data similar to what you got, as it would
>> > appear that your’s actually contains relevant gene/protein expression info.
>> >
>> > On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
>> > [hidden email]> wrote:
>> >
>> > > Once you have your TSV files just use something as
>> > >
>> > > x = read.table('protein_expression.tsv', h = T, sep = '\t')
>> > >
>> > > Do not copy paste the code of this email because it is formatted and would
>> > > not work in R.
>> > >
>> > >
>> > > Best
>> > >
>> > > F
>> > >
>> > > PS the data looks like this to me
>> > >
>> > > head(x)
>> > >   icgc_donor_id project_code icgc_specimen_id icgc_sample_id
>> > >  submitted_sample_id analysis_id        antibody_id gene_name
>> > > 1       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
>> > > 2       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
>> > > 3       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
>> > > 4       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
>> > > 5       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
>> > > 6       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
>> > >   gene_stable_id gene_build_version normalized_expression_level
>> > > verification_status verification_platform
>> > > 1             NA                 NA                  -1.1636330
>> > > not tested                    NA
>> > > 2             NA                 NA                  -1.7969721
>> > > not tested                    NA
>> > > 3             NA                 NA                  -0.7256390
>> > > not tested                    NA
>> > > 4             NA                 NA                   0.6498421
>> > > not tested                    NA
>> > > 5             NA                 NA                  -1.0262844
>> > > not tested                    NA
>> > > 6             NA                 NA                   1.5186400
>> > > not tested                    NA
>> > >                                         platform
>> > > 1 M.D. Anderson Reverse Phase Protein Array Core
>> > > 2 M.D. Anderson Reverse Phase Protein Array Core
>> > > 3 M.D. Anderson Reverse Phase Protein Array Core
>> > > 4 M.D. Anderson Reverse Phase Protein Array Core
>> > > 5 M.D. Anderson Reverse Phase Protein Array Core
>> > > 6 M.D. Anderson Reverse Phase Protein Array Core
>> > >
>> > >
>> > >
>> > > experimental_protocol
>> > > 1 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 2 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 3 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 4 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 5 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 6 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > >   raw_data_repository          raw_data_accession
>> > > 1                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 2                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 3                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 4                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 5                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 6                TCGA TCGA-19-5960-01A-13-1900-20
>> > >
>>
>>
>> --
>> Sarah Goslee (she/her)
>> http://www.numberwright.com

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: you are making it far too difficult

Spencer Brackett
Thank you!

On Thu, Dec 27, 2018 at 4:43 PM Sarah Goslee <[hidden email]> wrote:

> \t is the symbol for a tab.
> /t is two characters just as it seems. It's highly unlikely your file
> is delimited with /t, which would look like
> 1/t2/t3
>
> The help for read.table mentions this tangentially as part of
> read.delim(), and you can find out more under ?regex - see the section
> about escaping non-metacharacters with a backslash.
>
> Sarah
>
> On Thu, Dec 27, 2018 at 4:09 PM Spencer Brackett
> <[hidden email]> wrote:
> >
> > What is the significance of using / or \ ?
> >
> > On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <[hidden email]>
> wrote:
> >>
> >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
> >> <[hidden email]> wrote:
> >> >
> >> > Thank you for the help! I tried using the read.table command in my
> RStudio
> >> > using the following argument, and managed to open the file.
> >> >
> >> > GBM_protein_expression<-read.table(file.choose(), header=TRUE,
> sep=“/t”)
> >>
> >> Note that sep="/t" is NOT the same thing as the sep="\t" you were
> >> advised to use.
> >>
> >>
> >>
> >>
> >> >
> >> > However, my data did not unpack as yours did. I again only received a
> table
> >> > of true and flase distinctions per column, and my environment tab
> says that
> >> > there is 0 observations upon 0 variables.
> >> >
> >> > I believe I should be getting data similar to what you got, as it
> would
> >> > appear that your’s actually contains relevant gene/protein expression
> info.
> >> >
> >> > On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
> >> > [hidden email]> wrote:
> >> >
> >> > > Once you have your TSV files just use something as
> >> > >
> >> > > x = read.table('protein_expression.tsv', h = T, sep = '\t')
> >> > >
> >> > > Do not copy paste the code of this email because it is formatted
> and would
> >> > > not work in R.
> >> > >
> >> > >
> >> > > Best
> >> > >
> >> > > F
> >> > >
> >> > > PS the data looks like this to me
> >> > >
> >> > > head(x)
> >> > >   icgc_donor_id project_code icgc_specimen_id icgc_sample_id
> >> > >  submitted_sample_id analysis_id        antibody_id gene_name
> >> > > 1       DO12370       GBM-US          SP26475       SA131594
> >> > > TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
> >> > > 2       DO12370       GBM-US          SP26475       SA131594
> >> > > TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
> >> > > 3       DO12370       GBM-US          SP26475       SA131594
> >> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
> >> > > 4       DO12370       GBM-US          SP26475       SA131594
> >> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
> >> > > 5       DO12370       GBM-US          SP26475       SA131594
> >> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
> >> > > 6       DO12370       GBM-US          SP26475       SA131594
> >> > > TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
> >> > >   gene_stable_id gene_build_version normalized_expression_level
> >> > > verification_status verification_platform
> >> > > 1             NA                 NA                  -1.1636330
> >> > > not tested                    NA
> >> > > 2             NA                 NA                  -1.7969721
> >> > > not tested                    NA
> >> > > 3             NA                 NA                  -0.7256390
> >> > > not tested                    NA
> >> > > 4             NA                 NA                   0.6498421
> >> > > not tested                    NA
> >> > > 5             NA                 NA                  -1.0262844
> >> > > not tested                    NA
> >> > > 6             NA                 NA                   1.5186400
> >> > > not tested                    NA
> >> > >                                         platform
> >> > > 1 M.D. Anderson Reverse Phase Protein Array Core
> >> > > 2 M.D. Anderson Reverse Phase Protein Array Core
> >> > > 3 M.D. Anderson Reverse Phase Protein Array Core
> >> > > 4 M.D. Anderson Reverse Phase Protein Array Core
> >> > > 5 M.D. Anderson Reverse Phase Protein Array Core
> >> > > 6 M.D. Anderson Reverse Phase Protein Array Core
> >> > >
> >> > >
> >> > >
> >> > > experimental_protocol
> >> > > 1 MDA_RPPA_Core
> >> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >> > > 2 MDA_RPPA_Core
> >> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >> > > 3 MDA_RPPA_Core
> >> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >> > > 4 MDA_RPPA_Core
> >> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >> > > 5 MDA_RPPA_Core
> >> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >> > > 6 MDA_RPPA_Core
> >> > >
> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
> >> > >   raw_data_repository          raw_data_accession
> >> > > 1                TCGA TCGA-19-5960-01A-13-1900-20
> >> > > 2                TCGA TCGA-19-5960-01A-13-1900-20
> >> > > 3                TCGA TCGA-19-5960-01A-13-1900-20
> >> > > 4                TCGA TCGA-19-5960-01A-13-1900-20
> >> > > 5                TCGA TCGA-19-5960-01A-13-1900-20
> >> > > 6                TCGA TCGA-19-5960-01A-13-1900-20
> >> > >
> >>
> >>
> >> --
> >> Sarah Goslee (she/her)
> >> http://www.numberwright.com
>

        [[alternative HTML version deleted]]

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Re: you are making it far too difficult

Spencer Brackett
In reply to this post by Spencer Brackett
For future reference,

I unpacked the full gene expression file from ICGC by directly downloading
the following link
protein_expression.GBM-US.tsv.gz, and then using the argument Mr. Heiberger
layed out.

Best,

Spencer Brackett

On Thu, Dec 27, 2018 at 4:30 PM Spencer Brackett <
[hidden email]> wrote:

> Mr. Heiberger,
>
>   I followed your argument and it works. I received the same data. And
> yes, ICGC breakes their datasets into separate files based on data type.
> Thank you for the pointer on selecting all 50 rows, as I assumed that the
> entirety of gene expression data within the data set would be downloaded
> through the process you followed, as it does when directly downloading the
> file via a tsv.gz download.
>
> On Thu, Dec 27, 2018 at 4:05 PM Richard M. Heiberger <[hidden email]>
> wrote:
>
>> I downloaded the Donors dataset
>>
>>
>> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D
>>
>> by clicking "Export table as TSV".
>>
>> Then I read it with
>>
>> donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv")
>>
>> Here is the transcript.
>>
>> > donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv")
>> > donors
>>    Donor.ID Project.Code Primary.Site Gender Age.at.Diagnosis
>> 1   DO10892       GBM-US        Brain Female               45
>> 2   DO12328       GBM-US        Brain   Male               56
>> 3   DO11657       GBM-US        Brain Female               73
>> 4   DO13510       GBM-US        Brain Female               63
>> 5   DO12670       GBM-US        Brain Female               63
>> 6   DO11501       GBM-US        Brain Female               59
>> 7   DO13809       GBM-US        Brain Female               74
>> 8   DO13647       GBM-US        Brain   Male               56
>> 9   DO11645       GBM-US        Brain   Male               73
>> 10  DO14145       GBM-US        Brain Female               85
>>    Tumor.Stage.at.Diagnosis Survival.Time..days.  SSM CNSM  STSM   SGV
>> METH.A
>> 1                        NA                   NA True True False False
>>  True
>> 2                        NA                  154 True True False False
>>  True
>> 3                        NA                   NA True True False False
>>  True
>> 4                        NA                 1448 True True False False
>>  True
>> 5                        NA                  772 True True False False
>>  True
>> 6                        NA                   NA True True False False
>>  True
>> 7                        NA                  213 True True False False
>>  True
>> 8                        NA                  383 True True False False
>>  True
>> 9                        NA                  113 True True False False
>>  True
>> 10                       NA                   94 True True False False
>>  True
>>    METH.S EXP.A EXP.S PEXP miRNA.S   JCN Mutations Mutated.Genes
>> 1   False  True  True True   False False       269           392
>> 2   False  True False True   False False       192           263
>> 3   False  True False True   False False       128           209
>> 4   False  True  True True   False False       130           199
>> 5   False  True  True True   False False       142           194
>> 6   False  True  True True   False False       129           190
>> 7   False  True False True   False False       130           178
>> 8   False  True False True   False False       116           175
>> 9   False  True False True   False False       125           174
>> 10  False  True  True True   False False       108           169
>> >
>>
>> I don't know how to get the download of the whole file.  It looks like
>> you could page through it with the page menu at the bottom of the webpage.
>> If you do that, set it for 50 at a time instead of the default 10.
>>
>> For the Genes and the two types of Mutation files, it will be more
>> nuisance this way because there are about 10000 rows for each of those
>> three files, thus about 200 of these statements per dataset.
>>
>> I think it is time to move to the bioconductor list for specific guidance
>> on this type of dataset.
>>
>>
>> On Thu, Dec 27, 2018 at 3:28 PM Spencer Brackett <
>> [hidden email]> wrote:
>>
>>> Mr. Calboli,
>>>
>>> After beginning to unpack the GBM file you sent me via directly importing
>>> it unit my console, I received the following:
>>>
>>> View(GBM_PEXP.tsv)
>>>
>>> **Note that I named the file GBM_PEXP.tsv)**
>>>
>>>   Upon downloading, my script now contains a 2 by 2 table, with the x
>>> column still containing encoded script. As for my Data summary to the
>>>  right, this new file reports that 2 objects are acting upon 1 variable.
>>> How should I proceed?
>>>
>>> -Spencer
>>>
>>> On Thu, Dec 27, 2018 at 3:12 PM Federico Calboli <
>>> [hidden email]> wrote:
>>>
>>> > Unpack these files.
>>> >
>>> > F
>>> >
>>> >
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>

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Re: you are making it far too difficult

Caitlin Gibbons
In reply to this post by Spencer Brackett
I would :)


Sent from my iPhone

> On Dec 27, 2018, at 2:34 PM, Spencer Brackett <[hidden email]> wrote:
>
> So I should use “\t” proceeding on?
>
>> On Thu, Dec 27, 2018 at 4:30 PM Caitlin Gibbons <[hidden email]> wrote:
>> “\t” is an escape sequence which signifies one tab character. “/t” is NOT an escape sequence, and to R, looks like a very brief file path.
>>
>> Sent from my iPhone
>>
>> > On Dec 27, 2018, at 2:09 PM, Spencer Brackett <[hidden email]> wrote:
>> >
>> > What is the significance of using / or \ ?
>> >
>> >> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <[hidden email]> wrote:
>> >>
>> >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
>> >> <[hidden email]> wrote:
>> >>>
>> >>> Thank you for the help! I tried using the read.table command in my
>> >> RStudio
>> >>> using the following argument, and managed to open the file.
>> >>>
>> >>> GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)
>> >>
>> >> Note that sep="/t" is NOT the same thing as the sep="\t" you were
>> >> advised to use.
>> >>
>> >>
>> >>
>> >>
>> >>>
>> >>> However, my data did not unpack as yours did. I again only received a
>> >> table
>> >>> of true and flase distinctions per column, and my environment tab says
>> >> that
>> >>> there is 0 observations upon 0 variables.
>> >>>
>> >>> I believe I should be getting data similar to what you got, as it would
>> >>> appear that your’s actually contains relevant gene/protein expression
>> >> info.
>> >>>
>> >>> On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
>> >>> [hidden email]> wrote:
>> >>>
>> >>>> Once you have your TSV files just use something as
>> >>>>
>> >>>> x = read.table('protein_expression.tsv', h = T, sep = '\t')
>> >>>>
>> >>>> Do not copy paste the code of this email because it is formatted and
>> >> would
>> >>>> not work in R.
>> >>>>
>> >>>>
>> >>>> Best
>> >>>>
>> >>>> F
>> >>>>
>> >>>> PS the data looks like this to me
>> >>>>
>> >>>> head(x)
>> >>>>  icgc_donor_id project_code icgc_specimen_id icgc_sample_id
>> >>>> submitted_sample_id analysis_id        antibody_id gene_name
>> >>>> 1       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
>> >>>> 2       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
>> >>>> 3       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
>> >>>> 4       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
>> >>>> 5       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
>> >>>> 6       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
>> >>>>  gene_stable_id gene_build_version normalized_expression_level
>> >>>> verification_status verification_platform
>> >>>> 1             NA                 NA                  -1.1636330
>> >>>> not tested                    NA
>> >>>> 2             NA                 NA                  -1.7969721
>> >>>> not tested                    NA
>> >>>> 3             NA                 NA                  -0.7256390
>> >>>> not tested                    NA
>> >>>> 4             NA                 NA                   0.6498421
>> >>>> not tested                    NA
>> >>>> 5             NA                 NA                  -1.0262844
>> >>>> not tested                    NA
>> >>>> 6             NA                 NA                   1.5186400
>> >>>> not tested                    NA
>> >>>>                                        platform
>> >>>> 1 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 2 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 3 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 4 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 5 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 6 M.D. Anderson Reverse Phase Protein Array Core
>> >>>>
>> >>>>
>> >>>>
>> >>>> experimental_protocol
>> >>>> 1 MDA_RPPA_Core
>> >>>>
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 2 MDA_RPPA_Core
>> >>>>
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 3 MDA_RPPA_Core
>> >>>>
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 4 MDA_RPPA_Core
>> >>>>
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 5 MDA_RPPA_Core
>> >>>>
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 6 MDA_RPPA_Core
>> >>>>
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>>  raw_data_repository          raw_data_accession
>> >>>> 1                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 2                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 3                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 4                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 5                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 6                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>>
>> >>
>> >>
>> >> --
>> >> Sarah Goslee (she/her)
>> >> http://www.numberwright.com
>> >>
>> >
>> >    [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.

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