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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GSEA package error
3 messages · Pascal Oettli, Sébastien Bihorel
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 ?crit :
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.
it's the GSCA package....i made a typo in the subject, my apologies the package is available from here http://www.biostat.wisc.edu/~kendzior/GSCA/ i am now trying to do co-expression analysis using EBcoexpress but looks like i have a similar problem due to the sample size! thanks! -- View this message in context: http://r.789695.n4.nabble.com/GSEA-package-error-tp4651223p4651310.html Sent from the R help mailing list archive at Nabble.com.