I have two bulk RNA-Seq samples, already tpm-normalized.
I would like to know what is a reasonable normalization procedure to enable downstream log fold-change estimation.
The distribution of the two samples using the common set of genes looks similar:
However, the two samples have only been tpm-normalized, is it enough to guarantee reliable fold-change estimation? Should I use another normalization procedure, e.g. Quantile Normalization, before comparison?
My objective is to define a signature using the genes that are up-regulated in Sample1 with respect to Sample0, and vice versa. I'm using log fold-changes, but I'm concerned that their value may be affected by each sample distribution.
Do you also have suggestions for the definition of up-regulated genes with these data?