doubt about samr siggenes.table$genes.up

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doubt about samr siggenes.table$genes.up

Leonardo K
Hi, here's my siggenes.table$genes.up snippet.

Two class unpaired SAMR analysis.

"Row" "Gene ID" "Gene Name" "Score(d)" "Numerator(r)" "Denominator(s+s0)" "Fold Change" "q-value(%)"
"1" "25" "RPL15P22" "RPL15P22" "-1.44115338424578" "-18" "12.4899959967968" "1.27368448239355" "0"
"2" "47" "CHAF1A" "CHAF1A" "-1.44115338424578" "-18" "12.4899959967968" "1.30356683838951" "0"
"3" "48" "PARP2" "PARP2" "-1.44115338424578" "-18" "12.4899959967968" "1.09780831177589" "0"
"4" "52" "HMGXB4" "HMGXB4" "-1.44115338424578" "-18" "12.4899959967968" "1.22596090318945" "0"

Why do I get one column more in the data block (9) than the header (8)?

Looks like the second column (25,47,48,etc) does not make sense.

TIA

Leo
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Re: doubt about samr siggenes.table$genes.up

Peter Ehlers
On 2010-05-25 10:54, Leonardo K wrote:

>
> Hi, here's my siggenes.table$genes.up snippet.
>
> Two class unpaired SAMR analysis.
>
> "Row" "Gene ID" "Gene Name" "Score(d)" "Numerator(r)" "Denominator(s+s0)"
> "Fold Change" "q-value(%)"
> "1" "25" "RPL15P22" "RPL15P22" "-1.44115338424578" "-18" "12.4899959967968"
> "1.27368448239355" "0"
> "2" "47" "CHAF1A" "CHAF1A" "-1.44115338424578" "-18" "12.4899959967968"
> "1.30356683838951" "0"
> "3" "48" "PARP2" "PARP2" "-1.44115338424578" "-18" "12.4899959967968"
> "1.09780831177589" "0"
> "4" "52" "HMGXB4" "HMGXB4" "-1.44115338424578" "-18" "12.4899959967968"
> "1.22596090318945" "0"
>
> Why do I get one column more in the data block (9) than the header (8)?
>
> Looks like the second column (25,47,48,etc) does not make sense.
>

Presumably you are getting this from an application of write.table?
If so, use the argument 'row.names = FALSE' to remove the *first*
column. See the first sentence in the 'CSV files' section of
?write.table.

Your second column is part of the data you're saving (probably
rownames from a larger dataframe or matrix).

  -Peter Ehlers

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Re: doubt about samr siggenes.table$genes.up

Shi, Tao
Leo,

This question is more suited for the BioC help list.  Please post your question over there.

Also, offer more info about how you arrived this siggenes.table, what version of R and siggenes package you're using would be helpful.  Please read the posting guide!

...Tao



----- Original Message ----

> From: Peter Ehlers <[hidden email]>
> To: Leonardo K <[hidden email]>
> Cc: [hidden email]
> Sent: Tue, May 25, 2010 1:41:36 PM
> Subject: Re: [R] doubt about samr siggenes.table$genes.up
>
> On 2010-05-25 10:54, Leonardo K wrote:
>
> Hi, here's my
> siggenes.table$genes.up snippet.
>
> Two class unpaired SAMR
> analysis.
>
> "Row" "Gene ID" "Gene Name" "Score(d)" "Numerator(r)"
> "Denominator(s+s0)"
> "Fold Change" "q-value(%)"
> "1" "25"
> "RPL15P22" "RPL15P22" "-1.44115338424578" "-18" "12.4899959967968"
>
> "1.27368448239355" "0"
> "2" "47" "CHAF1A" "CHAF1A" "-1.44115338424578"
> "-18" "12.4899959967968"
> "1.30356683838951" "0"
> "3" "48" "PARP2"
> "PARP2" "-1.44115338424578" "-18" "12.4899959967968"
> "1.09780831177589"
> "0"
> "4" "52" "HMGXB4" "HMGXB4" "-1.44115338424578" "-18"
> "12.4899959967968"
> "1.22596090318945" "0"
>
> Why do I get
> one column more in the data block (9) than the header (8)?
>
> Looks
> like the second column (25,47,48,etc) does not make
> sense.
>

Presumably you are getting this from an application of
> write.table?
If so, use the argument 'row.names = FALSE' to remove the
> *first*
column. See the first sentence in the 'CSV files' section
> of
?write.table.

Your second column is part of the data you're saving
> (probably
rownames from a larger dataframe or matrix).

  -Peter
> Ehlers

______________________________________________

> ymailto="mailto:[hidden email]"
> href="mailto:[hidden email]">[hidden email] mailing list

> href="https://stat.ethz.ch/mailman/listinfo/r-help" target=_blank
> >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.

______________________________________________
[hidden email] mailing list
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.