[Bioc-devel] Does it matter whether I pool technical replicates for edgeR

[Ryan C. Thompson]

Hi all,

I'm working with an RNA-seq dataset where every biological sample has 
two technical replicates. Is important for me to merge the technical 
replicates so that my count matrix has exactly one column per biological 
sample, or is it ok to leave them separate? My worry would be that 
leaving them separate might make edgeR think that the technical 
replicates are biological replicates, leading to an underestimate of 
dispersion and overestiamte of significance.

So does it matter whether I pool technical replicates (by simply adding 
their counts together)? Is edgeR expected to give different results 
depending on whether or not I pool?

-Ryan Thompson