Hi, I would like to apply edgeR TMM normalization without converting data format into "DGEList", in other words I would like to manipulate the raw count table. (By doing so I can get a feeling about the whole RNAseq analysis procedure).
May I ask that if I just do the following:
(Raw count table)*(norm.factor), where norm.factor=edgeR::calcNormFactors((Raw count table),method='TMM').
And then conduct downstream analysis. Does this procedure make sense? After downstream analysis, can I say that I have applied TMM method for normalisation?
If the above procedure does not make sense, how about the following procedure:
(Raw count table)/((norm.factor)*colSums((Raw count table))), where
colSums((Raw count table)) stands for library size (each column represents a sample or a cell)
Thank you very much!