I have performed followed the Tophat alignment and Cufflinks differential analysis pipelines for my RNAseq data. I am not playing around in R with Cummerbund - I can produce pretty nice volcano plots and extract lists of significant genes.
I was wondering what the best way to produce a heatmap of z-scores using the cufflinks output is?
Appreciate all your suggestions.
(I have searched for about an hour to find an 'easy' solution, however cannot find one to my skill level, without being an R expert...).