Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

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Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

Spencer Brackett
Good evening,

I downloaded the Biobase package in order to utilize the ExpressionSet and
other features hosted there to examine annotations for probeset data, which
I seek to visualize. I currently have pre-analyzed object located in my
environment containing said probeset info, along with gene id and location.
After experimenting with the following approaches, I'm am at a loss for as
to why the AnnotatedDataFrame function is not being recognized by R.

##Example of some of my attempts and their respective error messages##

>AnnotatedDataFrame()
    Error in AnnotatedDataFrame() : could not find function
   "AnnotatedDataFrame"

 signature(object="assayData")
     object  "assayData"
> annotatedDataFrameFrom("assayData", byrow=FALSE)
Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
  could not find function "annotatedDataFrameFrom"

>as(data.frame, "AnnotatedDataFrame")
Error in as(data.frame, "AnnotatedDataFrame") :
  no method or default for coercing “function” to “AnnotatedDataFrame”

Best,

Spencer

        [[alternative HTML version deleted]]

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Re: Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

Martin Morgan-4
Are you remembering to attach the Biobase package to your R session?

> AnnotatedDataFrame()
Error in AnnotatedDataFrame() :
  could not find function "AnnotatedDataFrame"
> suppressPackageStartupMessages({ library(Biobase) })
> AnnotatedDataFrame()
An object of class 'AnnotatedDataFrame': none

Biobase is a Bioconductor package, so support questions should more appropriately go to https://support.bioconductor.org

Martin

On 7/17/19, 4:20 PM, "R-help on behalf of Spencer Brackett" <[hidden email] on behalf of [hidden email]> wrote:

    Good evening,
   
    I downloaded the Biobase package in order to utilize the ExpressionSet and
    other features hosted there to examine annotations for probeset data, which
    I seek to visualize. I currently have pre-analyzed object located in my
    environment containing said probeset info, along with gene id and location.
    After experimenting with the following approaches, I'm am at a loss for as
    to why the AnnotatedDataFrame function is not being recognized by R.
   
    ##Example of some of my attempts and their respective error messages##
   
    >AnnotatedDataFrame()
        Error in AnnotatedDataFrame() : could not find function
       "AnnotatedDataFrame"
   
     signature(object="assayData")
         object  "assayData"
    > annotatedDataFrameFrom("assayData", byrow=FALSE)
    Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
      could not find function "annotatedDataFrameFrom"
   
    >as(data.frame, "AnnotatedDataFrame")
    Error in as(data.frame, "AnnotatedDataFrame") :
      no method or default for coercing “function” to “AnnotatedDataFrame”
   
    Best,
   
    Spencer
   
    [[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.
   
______________________________________________
[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: Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

Spencer Brackett
I thought it successfully loaded after library(Biobase) but after
implementing your suggested I got the following....

Error in library(Biobase) : there is no package called ‘Biobase’

So to download it would I try to rerun with Debug? This is an option given
as part of the return



On Wed, Jul 17, 2019 at 4:37 PM Martin Morgan <[hidden email]>
wrote:

> Are you remembering to attach the Biobase package to your R session?
>
> > AnnotatedDataFrame()
> Error in AnnotatedDataFrame() :
>   could not find function "AnnotatedDataFrame"
> > suppressPackageStartupMessages({ library(Biobase) })
> > AnnotatedDataFrame()
> An object of class 'AnnotatedDataFrame': none
>
> Biobase is a Bioconductor package, so support questions should more
> appropriately go to https://support.bioconductor.org
>
> Martin
>
> On 7/17/19, 4:20 PM, "R-help on behalf of Spencer Brackett" <
> [hidden email] on behalf of [hidden email]>
> wrote:
>
>     Good evening,
>
>     I downloaded the Biobase package in order to utilize the ExpressionSet
> and
>     other features hosted there to examine annotations for probeset data,
> which
>     I seek to visualize. I currently have pre-analyzed object located in my
>     environment containing said probeset info, along with gene id and
> location.
>     After experimenting with the following approaches, I'm am at a loss
> for as
>     to why the AnnotatedDataFrame function is not being recognized by R.
>
>     ##Example of some of my attempts and their respective error messages##
>
>     >AnnotatedDataFrame()
>         Error in AnnotatedDataFrame() : could not find function
>        "AnnotatedDataFrame"
>
>      signature(object="assayData")
>          object  "assayData"
>     > annotatedDataFrameFrom("assayData", byrow=FALSE)
>     Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
>       could not find function "annotatedDataFrameFrom"
>
>     >as(data.frame, "AnnotatedDataFrame")
>     Error in as(data.frame, "AnnotatedDataFrame") :
>       no method or default for coercing “function” to “AnnotatedDataFrame”
>
>     Best,
>
>     Spencer
>
>         [[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]]

______________________________________________
[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: Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

Bert Gunter-2
In reply to this post by Spencer Brackett
Isn't this a Bioconductor package? If so, shouldn't you be posting on their
website instead of here?
(Apologies if I'm mistaken).


Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Wed, Jul 17, 2019 at 1:20 PM Spencer Brackett <
[hidden email]> wrote:

> Good evening,
>
> I downloaded the Biobase package in order to utilize the ExpressionSet and
> other features hosted there to examine annotations for probeset data, which
> I seek to visualize. I currently have pre-analyzed object located in my
> environment containing said probeset info, along with gene id and location.
> After experimenting with the following approaches, I'm am at a loss for as
> to why the AnnotatedDataFrame function is not being recognized by R.
>
> ##Example of some of my attempts and their respective error messages##
>
> >AnnotatedDataFrame()
>     Error in AnnotatedDataFrame() : could not find function
>    "AnnotatedDataFrame"
>
>  signature(object="assayData")
>      object  "assayData"
> > annotatedDataFrameFrom("assayData", byrow=FALSE)
> Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
>   could not find function "annotatedDataFrameFrom"
>
> >as(data.frame, "AnnotatedDataFrame")
> Error in as(data.frame, "AnnotatedDataFrame") :
>   no method or default for coercing “function” to “AnnotatedDataFrame”
>
> Best,
>
> Spencer
>
>         [[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]]

______________________________________________
[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: Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

Spencer Brackett
It is. I will try their mailing list :)

On Wed, Jul 17, 2019 at 4:56 PM Bert Gunter <[hidden email]> wrote:

> Isn't this a Bioconductor package? If so, shouldn't you be posting on
> their website instead of here?
> (Apologies if I'm mistaken).
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Wed, Jul 17, 2019 at 1:20 PM Spencer Brackett <
> [hidden email]> wrote:
>
>> Good evening,
>>
>> I downloaded the Biobase package in order to utilize the ExpressionSet and
>> other features hosted there to examine annotations for probeset data,
>> which
>> I seek to visualize. I currently have pre-analyzed object located in my
>> environment containing said probeset info, along with gene id and
>> location.
>> After experimenting with the following approaches, I'm am at a loss for as
>> to why the AnnotatedDataFrame function is not being recognized by R.
>>
>> ##Example of some of my attempts and their respective error messages##
>>
>> >AnnotatedDataFrame()
>>     Error in AnnotatedDataFrame() : could not find function
>>    "AnnotatedDataFrame"
>>
>>  signature(object="assayData")
>>      object  "assayData"
>> > annotatedDataFrameFrom("assayData", byrow=FALSE)
>> Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
>>   could not find function "annotatedDataFrameFrom"
>>
>> >as(data.frame, "AnnotatedDataFrame")
>> Error in as(data.frame, "AnnotatedDataFrame") :
>>   no method or default for coercing “function” to “AnnotatedDataFrame”
>>
>> Best,
>>
>> Spencer
>>
>>         [[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]]

______________________________________________
[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.