Hi!

I would like to know if it is possible to extract the RLE normalized count table after the CalcNormFactors and how I can extract it.

Enrichetta

Although you haven't explicitly said so, I guess you're in "edgeR" land and I will assume you have a DGEList that you've properly setup. So let's say you've done:

y <- DGEList(...)
y <- calcNormFactors(y, 'RLE')

and now you want to get the normalized counts out, you could simply get the counts-per-million and multiply that matrix by a million, eg:

ncounts <- cpm(y) * 1e6