[BioC] GSVA: using Entrez ID's as identifiers

[Robert Castelo]

hi Wendy,

sorry for my late answer. in principle there is no problem for the
gsva() function to take Entrez IDs in your expression data matrix.

if the expression data comes as a matrix, and rows are annotated with
Entrez IDs and the gene sets are also annotated with Entrez IDs, there
should be absolutely no problem.

if the expression data comes as an ExpressionSet object where the
'features' are not Affy probe IDs but just EntrezIDs. just make sure
that the annotation slot has the corresponding organism-level package.
for instance, in the case of human:

annotation(eset) <- "org.Hs.eg.db"

let me know if you have any problem with this.

cheers,
robert.

On Fri, 2011-11-11 at 14:44 -0500, Wendy Qiao wrote:
> Hi all,
> 
> I am using the GSVA package for some analysis. I found that the package
> only takes the gene expression matrix annotated with affymetrix probe IDs,
> although the gene set collection is made of Entrez IDs. I imagine there a
> step in the package for converting the Affymetrix probe IDs to Entrez IDs.
> As my data are from the Illumina platform, I am wondering if an expression
> matrix annotated with Entrez IDs can be used directly.
> 
> Thank you,
> Wendy
> 
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