Can somebody tell me how to add annotation to an affy exprSet? I
would like to see the gene name in the limma topTable output. I
looked at the annotate documentation and tried all kind of
manipulations on the hgu133plus2 datafile, but I can't get it to work.
Hope you can help.
Many thanks
Andreas
In the limma Vignette chapter 21.2, the ApoAI dataset contains gene
names. How did they get in there? This is exactly what I am trying to
achieve.
Thanks
Andreas
>Can somebody tell me how to add annotation to an affy exprSet? I
>would like to see the gene name in the limma topTable output. I
>looked at the annotate documentation and tried all kind of
>manipulations on the hgu133plus2 datafile, but I can't get it to
>work.
>
>Hope you can help.
>Many thanks
>Andreas
Andreas Zankl wrote:
> In the limma Vignette chapter 21.2, the ApoAI dataset contains gene
> names. How did they get in there? This is exactly what I am trying
to
> achieve.
You could use the genelist argument of topTable. I wouldn't recommend
using the actual gene name, because they can be quite long - instead I
would use the gene symbol. However the choice is up to you.
genenames <- sapply(mget(ls(hgu133plus2GENENAME), hgu133plus2GENENAME,
ifnotfound = NA), function(x) x[1])
topTable(fit, genelist = genenames)
For the symbol, you do the above but substitute hgu133plus2SYMBOL.
HTH,
Jim
>
> Thanks
> Andreas
>
>
>>Can somebody tell me how to add annotation to an affy exprSet? I
>>would like to see the gene name in the limma topTable output. I
>>looked at the annotate documentation and tried all kind of
>>manipulations on the hgu133plus2 datafile, but I can't get it to
>>work.
>>
>>Hope you can help.
>>Many thanks
>>Andreas
>
>
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
