Dear All,

I am currently analyzing an RNASeq dataset, I have 3 samples with n=4 each.
I was exploring the performance of both EdgeR and DeSeq and I noticed they
vary a lot on the dispersion of the normalization factors.
Using EdgeR calcNormFactors I get a distribution that varies from 0.9-1.2
while if I use DeSeq estimateSizeFactors the distribution varies from
0.4-1.7. Given that these are exactly the same libraries
why do the estimates vary so much? How will that impact the list of DEgenes?
I know that the calculations are not performed in the same way, but aren't
those two functions aimed at estimating the same phenomenon?

thanks for your help.

-- 
Lucia Peixoto PhD
Postdoctoral Research Fellow
Laboratory of Dr. Ted Abel
Department of Biology
School of Arts and Sciences
University of Pennsylvania

"Think boldly, don't be afraid of making mistakes, don't miss small
details, keep your eyes open, and be modest in everything except your
aims."
Albert Szent-Gyorgyi

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