I am working with edgeR to look at differential expression in a 2x2 design
of two populations with two treatments (a total of 4 groups with 6
replicates each).  I have very interesting results. However, a colleague
asked me the other day, "What does edgeR do with zero values for read count
data?"

I have an intermediate level of statistical understanding at best, and in
some instances, a novice level.  I am assuming that the negative binomial
model in some way accounts for tags with a large number of 0 cells.  Is
there something more going on the generalized linear model or in fitting
the negative binomial distribution that accounts for a large percentage of
zeros from some of the tags?

Thank you for your guidance!

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