I'm working with RNA-Seq data from a panel of around 50 samples from different strains from a non-model organism. I did the standard Cufflinks pipeline and am now using CummeRbund to do some differential expression analysis and am running into some complications.
Complication 1, many of the plots become difficult to read or difficult to even run with around 50 samples. For example, any matrix style plot becomes 50x50 and that just won't be pretty (if it ever finished that is). If I could subset, say 5 of these samples per experimental condition that would be much more manageable!
Complication 2, Is it possible to subset or group my samples? For example, I want to group all samples collected from the US, and group all samples collected from Europe and run individual analyses on each grouping (in addition to the overall analysis).
I've been trying to find the answer to this challenge but have been unsuccessful thus far (I see several instances of this question on seqanswers but no answers yet!)
Thanks!
