Hello everyone!

I'm using edgeR to detect DE genes on my data. I have 2 control samples and
4 mutated samples.
I understand why I should filter them and I know the command to use (the
tutorials Drs. Mark Robinson, Davs McCarthy, Yunshun Chen and Gordon
K.Smyth made are pretty self explanatory in everything). What I don't
understand however is the filtering criteria.

I named my DGE object as "d", so the command I'm using is:
d <- d[rowSums(1e+06 * d$counts/expandAsMatrix(d$samples$lib.size, dim(d))
> 1) >= ?, ]
Meaning that I'm filtering out genes that don't have at least one count per
million on "?" samples. What value should I use for "?" given that I have 2
control and 4 mutated samples.

Thank you in advance for your help!
C

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