q>1 in cuffdiff output

[kasutubh]

Hi,

I know this question has already been asked (http://seqanswers.com/forums/showthr...t=13764z)..but I'm very new to these things and didn't follow the R script..could anyone please break it up for me? Also, since we only select for genes with q<0.05 does it matter if some values are greater than one ( I mean would these genes end up having q<0.05 after the correction?)

Thanks!

[kasutubh]

Using version 1.3 of cufflinks solved the q>1 problem..but I also ended up having far less number of significant genes than the old data set now. Has anyone else encountered such a thing? Can use of different version of cufflinks reduce the number of significant genes (almost 10 times in this case)
Thanks!