I have counts data from a HTG Edge-Seq miRNA Whole Transcriptome experiment perfomed on plasma samples from patients.
I wonder if the mean normalization that DESEq2 does assumes that the global expression of miRNAs is identical between the conditions. For example, if my study condition causes a drop in global miRNA levels, could I see it after normalizing with DESeq2? Wouldn't this create an artificial scaling to match the global expression between samples?
In these samples no spike-in was added, is there any normalization method that does not start from the premise that the global expression is identical between samples?
Thanks in advance