[BioC] Problem with "ragene10stprobeset.db" package

[James W. MacDonald]

Hi Laura,

On 5/3/2012 7:03 AM, Laura Bermúdez wrote:
> Dear Bioconductor Team:
>
>
>
> I am using the Bioconductor annotation package "ragene10stprobeset.db" for
> an analysis of differential expression, but when I want to annotate my
> Arrays selection ("10700001" "10700005" "10700013" "10700063" ... etc..), it
> shows me “value for "10700063" not found”. Why can this happen?

You don't give us much to go on. In future, please give us some code and 
the results from running sessionInfo() at an R prompt.

If I break out my crystal ball, I can divine that you have done 
something like

library(oligo)
abatch <- read.celfiles(celfiles)
eset <- rma(abatch)

or

library(affy)
abatch <- ReadAffy()
eset <- rma(abatch)

In either case, what you have done is summarize data at the _transcript_ 
level. Note here that using oligo, you can also summarize at the 
probeset level, which is pretty close to summarizing by exon.

Since my crystal ball tells me you summarized at the transcript level, 
you will also need to annotate at the transcript level. In which case 
you need the ragene10sttranscriptcluster.db package.

Best,

Jim


>
>
>
> Thanks for your help.
>
>
>
> Laura
>
>
> 	[[alternative HTML version deleted]]
>
>
>
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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