Hi,

I hope to try a full library size normalization but with edgeR.

So I performed the following:

data(tamoxifen_analysis)
tamoxifen = dba.normalize(tamoxifen, method = DBA_EDGER)
dba.normalize(tamoxifen, method = DBA_EDGER, bRetrieve = T)

Interestingly the normalization factors are all 1

$norm.method
[1] "lib"

$norm.factors
 [1] 1 1 1 1 1 1 1 1 1 1 1

$lib.method
[1] "full"

$lib.sizes
 [1]  652697  663370  346429  368052  466273  399879 1475415  616630  593224  706836 2575408

But apparently some normalization has happened as the ma plot is different from the one using raw data:

tamoxifen = dba.analyze(tamoxifen, method = DBA_EDGER)
dba.plotMA(tamoxifen, method = DBA_EDGER)

Could you please explain why is that? Thanks!

You perform library normalization which is expected to return normalization factors being all 1. If you want to use the more elaborate edgeR normalization then you have to tell that to the function, see ?dba.normalize. Looking at the MA-plot and the discrepancy between the loess (red) and neutral line (blue) indeed suggests that normalization is not optimal here. You're probably overestimating differences that are higher in the responsive group.