[Bioc-devel] Does it matter whether I pool technical replicates for edgeR
Ryan C. Thompson
rct at thompsonclan.org
Thu Dec 6 20:29:23 CET 2012
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?
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