[R] GSEA package error

[Pascal Oettli]

Hello,

For clarification, is it 'GSEA' or 'GSCA' package?

And from where did you get it?

Regards,
Pascal


Le 29/11/2012 07:59, Seb a écrit :
> 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
>
>
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/GSEA-package-error-tp4651223.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>