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:
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