Hi Robert,

Thank you for your reply. I happened to convert all the genes to hgu95a
probe IDs as I found that this is the only platform that works with
ExpressionSet. It would be great that we could make the entrez ID works.
Following is my error that I got with your code.

Thank you.
Wendy

> BcellSet
ExpressionSet (storageMode: lockedEnvironment)
assayData: 12148 features, 7 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: Illumi_PREBCEL_1 Illumi_PREBCEL_2 ... Affy_PREBCEL_4 (7
total)
  varLabels: CellType Platform Replicates
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: org.Hs.eg.db
> preBcell.KEGG<-gsva(BcellSet,KEGGc2BroadSets,abs.ranking=FALSE)$es.obs
Mapping identifiers between gene sets and feature names
Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose =
verbose)) :
  error in evaluating the argument 'object' in selecting a method for
function 'GeneSetCollection': Error in get(mapName, envir = pkgEnv,
inherits = FALSE) :
  object 'org.Hs.egENTREZID' not found


On 14 November 2011 12:27, Robert Castelo <robert.castelo@upf.edu> wrote:

> 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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> >
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>
>

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