**30**wrote:

I am trying to get normalised RNASeq expression matrices using different methods.

I have a read count matrix:

> matrix sample1 sample2 sample3 gene1 13456 16172 13303 gene2 988 830 857 gene3 11780 13831 10550

And I calculated scaling factors with the 3 methods available from the EdgeR `calcNormFactors `

function:

> upQuartileFactors <- calcNormFactors(matrix, method="upperquartile", p=0.75) > upQuartileFactors sample1 sample2 sample3 0.9952710 1.0063954 0.9983665 > tmmFactors <- calcNormFactors(in_matrix, method="TMM") > tmmfactors [1] 0.9962241 1.0020331 1.0017536 > rleFactors <- calcNormFactors(in_matrix, method="RLE") > rleFactors sample1 sample2 sample3 1.0038347 0.9851548 1.0111914

QUESTIONS:

I do I get a normalised expression matrix for each of the normalisation method employed?

Can I do one of the following and for which method?

matrix / scaled_factors matrix * scaled_factors matrix / (library_size * scaled_factors)

**6.8k**• written 11 weeks ago by user31888 •

**30**