Hi Joe,

BrainArray provides annotation packages (*.db_version.tar.gz) for all custom CDFs and looks like you installed the correct one. According to the GSVA documentation, following code should work with GSVAdata:

gsva(eset, c2BroadSet, ...)

(probably requiring that annotation(eset) returns "primeviewhsentrezg") or

gsva(matrix, c2BroadSet, annotation="primeviewhsentrezg" ,...)

Alternatively, use these annotation packages to convert (i) your genesets to probeset ids or (ii) the probeset ids to the gene identifiers used in your genesets. For the latter:

symbols <- lookUp(featureNames(eset), annotation(eset), "SYMBOL")
featureNames(eset) <- symbols

Here the links to some useful gene sets in the GMT file format (there are lots of parsers in Bioconductor and CRAN, most simple to use is probably GSA::GSA.read.gmt. To get a similar gene set object as c2BroadSet, use the GSEABase package):

http://www.broadinstitute.org/gsea/msigdb/index.jsp
http://compbio.dfci.harvard.edu/genesigdb/downloadall.jsp

Cheers,
Markus

On Sep 5, 2013, at 8:48 PM, Dan Tenenbaum wrote:

> CC'ing GSVA maintainer.
> 
> On Thu, Sep 5, 2013 at 5:45 PM, Joe [guest] <guest@bioconductor.org> wrote:
>> 
>> I'm a GSVA package new user. One question make me confused. If I used custom CDF (download from BrainArray website), usually, the custom CDF file has unique ProbeID correspond to one gene, so this format expression data could be used in GSVA?
>> Another one, exclude c2BroadSet, is there any GeneSellection data could be used or download?
>> 
>> -- output of sessionInfo():
>> 
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> 
>> locale:
>> [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
>> [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
>> [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
>> 
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>> 
>> other attached packages:
>> [1] genefilter_1.42.0              primeviewhsentrezgprobe_17.1.0
>> [3] primeviewhsentrezg.db_17.1.0   org.Hs.eg.db_2.9.0
>> [5] RSQLite_0.11.4                 DBI_0.2-7
>> [7] primeviewhsentrezgcdf_17.1.0   AnnotationDbi_1.22.6
>> [9] Biobase_2.20.1                 BiocGenerics_0.6.0
>> [11] rj_1.1.3-1
>> 
>> loaded via a namespace (and not attached):
>> [1] annotate_1.38.0 IRanges_1.18.3  rj.gd_1.1.3-1   splines_3.0.1
>> [5] stats4_3.0.1    survival_2.37-4 tools_3.0.1     XML_3.98-1.1
>> [9] xtable_1.7-1
>> 
>> --
>> Sent via the guest posting facility at bioconductor.org.
>> 
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