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

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