Off topic:how to obtain a normalised expression matrix from read counts and scaling factors
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5.9 years ago
user31888 ▴ 130

I have a read count matrix (row: genes; column: samples) from which I generated scaling factors using EdgeR 'calcNormFactors' function, set with different methods ("TMM","RLE","upperquartile").

Now I have my raw read counts matrix and vectors of scaling factors for each samples.

How do I get a normalised expression matrix:

raw count / scaling factor

OR

raw count * scaling factor

OR

raw count / (library size * scaling factor)

or by another way?

Thanks for your explanations.

RNASeq normalisation • 1.7k views
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