[BioC] getSYMBOL( ) error

[Rao,Xiayu]

Oh, I see. Thank you very much for your kind help, James!

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at uw.edu] 
Sent: Tuesday, July 09, 2013 11:19 AM
To: Rao,Xiayu
Cc: 'bioconductor at r-project.org'
Subject: Re: [BioC] getSYMBOL( ) error

Hi Xaiyu,

On 7/8/2013 6:13 PM, Rao,Xiayu wrote:
> Hello,
>
> I tried to find gene names that match affyIDs, and I tried two ways as below, but neither worked. I got all NAs for the Symbol column. I have no idea what happened. Thank you very much for helping me out!
>
> (1) library(affy)
> mydata<- ReadAffy()
> eset<- rma(mydata)
> library(annotate)
> library(hgu95av2.db)
> ID<- featureNames(eset)
> Symbol<- getSYMBOL(ID,"hgu95av2.db")
> fData(eset)<- data.frame(ID=ID,Symbol=Symbol)
>
> All NAs for Symbol in the topTable
>
> (2) fit$genes$Symbol<- getSYMBOL(fit$genes$ID, "hgu95av2.db")
>
>> fit
> $genes
>         ID        Symbol
> 1 7892501     NA
> 2 7892502     NA
> 3 7892503     NA
> 4 7892504     NA
> 5 7892505     NA
> 32316 more rows ...

Those aren't hgu95av2 probe IDs. They appear to be hugene 1.0 transcript cluster IDs. So you need to use the hugene10sttranscriptcluster.db package.

Best,

Jim


>
> Thanks,
> Xiayu
>
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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