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.
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
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