I am trying to figure out the workflow when I want to select only a small part of the genome for DE-analysis. We want to select only a small part of all genes (1000 of +/- 60.000 genes). Following earlier posts I think the way to go would be to first normalize on all genes and then make a subset of these specific 1000 genes afterwards.
My question is whether I should keep the library sizes if I subset after normalization?
If I am correct I should keep lib.sizes after normalization, so
keep.lib.sizes = T.
When subsetting before normalization, keep.lib.sizes should be False. Does that make sense?