Hi James,

Thank you so much for your help. I am successfully building ens (had to
update to 2.15 to use select) but for some reason I am having problems
merging/binding the data into the same frame

> data.frame(ens, exprs(eset_rma), assayDataElement(eset_pma, "se.exprs"))
Error in data.frame(ens, exprs(eset_rma), assayDataElement(eset_pma,
"se.exprs")) :
  arguments imply differing number of rows: 46603, 45101

> merge(ens,exprs(eset_rma))
Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) :
  cannot allocate vector of length 2101841903

Any idea how I could resolve this issue?

Jens

On Tue, Oct 23, 2012 at 5:09 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Jens,
>
>
> On 10/23/2012 3:48 PM, Jens Lichtenberg [guest] wrote:
>
>> I am using the affy package to analyze a set of GSM files downloaded from
>> GEO. In addition to providing a table with probe ids, expression levels and
>> p values, I would like to have the ensembl ids associated with the probe
>> ids.
>>
>> I loaded in the corresponding platform data (in my case mouse4302) but I
>> am not quite sure how to go about the connection of the data.
>>
>> Here is the way I am building the analysis table:
>>
>>   -- output of sessionInfo():
>>
>> source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R>
>> ")
>> library(affy)
>>
>> filenames<- c("1.CEL","2.CEL")
>>
>> affy.data<- ReadAffy(filenames = as.character(filenames))
>> platform<- annotation(affy.data),".db"
>> biocLite(platform)
>> library(platform)
>>
>> eset_rma<- rma(affy.data)
>> eset_pma<- mas5calls(affy.data)
>> my_frame<- data.frame(exprs(eset_rma), assayDataElement(eset_pma,
>> "se.exprs"))
>> my_frame<- my_frame[, sort(names(my_frame))]
>> write.table(my_frame, file="export.tsv", sep="\t", col.names = NA)
>>
>
> ens <- select(mouse4302.db, featureNames(eset_pma), "ENSEMBL")
>
> If all the probeset IDs in 'ens' and 'my_frame' match up, you can simply
> cbind() to my_frame. I assume they will, but I would check to be sure.
> Otherwise you can just merge().
>
> Best,
>
> Jim
>
>
>
>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

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