[R] GSEA package error

Seb seba.bat at gmail.com
Wed Nov 28 23:59:45 CET 2012


Dear R gurus

I’m trying to use the GSCA package to a series of microarray data (prostate
cancer normal vs tumor (29 vs 29 paired)) but I’m running into some
problems.

I have a matrix (named /data_final/) with 11k rows(genes) and 60 cols (58
samples (29N vs 29T), GO IDs, KEGG IDs). 
I also have a separate vector GS with the GO IDs mapped to genes (no
duplicate genes but multiple IDs per gene like in col 59)

However when I try to run:
/singleDC(data_final, group=c(1:29,30,58), GSdefList = GS, nperm = 3,
permDI=TRUE)/

I get an error/ “unused argument(s) (permDI=TRUE)”/ 

When I run it without that argument it runs indefinitely even if I use only
100 rows data_final[1:100,].
Furthermore when I block the computation I get the error:

/Error in `[.data.frame`(fixed.gs.data, , (csum.group[i-1] +
1):csum.group[i]) :
                Undefined colums selected/


If you could give me some ideas on how to have it working that would be
extremely useful!

Seb




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