Normalization needed for RNAseq data analysis?

[aminzia]

Hi Mike,

Is there anywhere in SAM package that you'd perform between-sample normalization to account for different sequencing depth variation between samples? In other words, does SAM need un-normalized or normalized counts to perform the significance analysis?

Thank you
Amin

[SamGG]

Hi,
SAMseq is normalizing counts, see samr:::samr.estimate.depth().
Unfortunately, this is not an option and there is no way to pre-compute the scaling factors.
Best.