[BioC] Expected number of DE genes?

[Jessica Perry Hekman]

I'm getting only a few dozen differentially expressed genes when I 
analyze my RNA-Seq data with DESeq2 (79) and EdgeR (34) (even fewer when 
I use EBSeq). I had expected many more -- hundreds or even a thousand. 
If this is the real answer, I'm fine with it, but I'm concerned that I'm 
doing something wrong. What are the ranges of numbers of differentially 
expressed genes that one would expect from DESeq2 or EdgeR?

More information:

I'm in the midst of my first RNA-seq project (as many of you have 
probably surmised from my frequent postings to a variety of lists). My 
initial goal is to get a list of differentially expressed (DE) genes.

I have 24 samples, 12 from each of 2 treatment groups.

My species is fox (Vulpes vulpes), which aligns very nicely to dog 
(Canis familiaris).

My current approach is to use the dog reference genome (to which my fox 
reads align at about 83%) + GTF with location of exons.

Can I feel confident about DESeq2 and EdgeR's calls?

Thanks very much for any insights,

Jessica

-- 
Jessica P. Hekman, DVM, MS
PhD student, University of Illinois, Urbana-Champaign
Animal Sciences / Genetics, Genomics, and Bioinformatics