[BioC] Is there any prejudice whether to use edgeR or DESeq for differential expression analysis for RNA Seq data

[Steve Lianoglou]

Hi,

On Wed, Nov 7, 2012 at 9:42 AM, Sakshi Gulati
<Sakshi.Gulati at cancer.org.uk> wrote:
> Hi Mark,
>
> Thanks for answering. It makes more sense now. I have upper quartile normalised RSEM counts per gene. Is that ok as an input for edgeR and/or DESeq?

My guess is that they are not fine.

Not familiar with RSEM, but if these are actually *counts* (first hint
that they are not counts if they are not integers) then you are ok. If
these are something like (R|F)PKM, then you're not -- ditto if you are
already inputting numbers that have been previously scaled to library
size.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact