Good morning,

I am trying to understand the relative log expression normalizat

ion made by the DESEQ2 wrapper function.

As far as I understood, It corresponds to the computing of scaling factor as described by Anders and Hubers (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106):

"Hence, to estimate the size factors, we take the median of the ratios of observed counts. Generalizing the procedure just outlined to the case of more than two samples, we use:

sˆj=medianikij(∏mv=1kiv)1/m.

(5)

The denominator of this expression can be interpreted as a pseudo-reference sample obtained by taking the geometric mean across samples. Thus, each size factor estimate sˆj is computed as the median of the ratios of the j-th sample's counts to those of the pseudo-reference."

But there is non log transformation in that formula so I'm not sure it is the right description of the RLE normalization method.

Thank you for your answers

RLE is not terminology created by the DESeq/DESeq2 team.  All you need to know is that   both of these methods use the same normalization and the formula is given in both publications.