[BioC] DESeq and transcript-wise analysis

[Elena Sorokin]

Dear Simon, Abhi, and Martin,

Thanks for your replies. I just learned about DEXseq and am working 
through the vignette. Importantly for me, I see that DEXseq can also do 
generalized linear models. I will compare that to my current isoform 
analysis in DESeq with its GLM function, then compare both those to 
previous results from Cuffdiff, where unfortunately I've only been able 
to do 2-sample comparisons.

Simon, I'm working with C. elegans, not with a vertebrate, and am 
usually dealing with 1-2 isoforms per gene, though sometimes it can be 
much more. I don't know if that still presents a huge problem for DESeq, 
but I figure it's worth trying anyway.

Thanks again for everyone's advice. It is much appreciated! Best, Elena