[BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?

Chanchal Kumar chanchal at biochem.mpg.de
Fri Jul 25 01:14:20 CEST 2008

Dear All,

  I have a set of Entrez ids which have been ordered as per fold change
expression from a control experiment. I am now interested in carrying
out gene set enrichment analysis using Bioconductor GSEABase package. I
don't have any other statistics for these genes. Is it possible to carry
out GSEA on a vector of Entrezids which is ordered by say fold change? I
attach an example vector and would like to carry out GSEA on this test
set to get an idea of how this might work.

set1 <- unique(getEG(sample(ls(hgu95av2GO), 100), "hgu95av2"))
set1<-na.omit(set1) # as I get NAs in the vector before

For GSEA I assume that element set1[1] has highest fold change and
set1[length(set1)] has the lowest fold change. Any help in this regard
will be appreciated. Thanks in advance!


> sessionInfo()
R version 2.7.0 (2008-04-22) 


attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods

[8] base     

other attached packages:
[1] annotate_1.18.0     xtable_1.5-2        hgu95av2.db_2.2.0  
[4] AnnotationDbi_1.2.1 RSQLite_0.6-8       DBI_0.2-4          
[7] Biobase_2.0.1      

loaded via a namespace (and not attached):
[1] splines_2.7.0


Best Regards,
Chanchal Kumar, Ph.D. Candidate
Dept. of Proteomics and Signal Transduction
Max Planck Institute of Biochemistry
Am Klopferspitz 18
82152 D-Martinsried (near Munich)
e-mail: chanchal at biochem.mpg.de
Phone: (Office) +49 (0) 89 8578 2296
Fax:(Office) +49 (0) 89 8578 2219

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