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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