Hi everyone,

My question is more conceptual than practical. Right now, I am analysing differentially expressed genes in different immune cell types coming from different organs. I want to compare cell types within organs and also between organs (same type in different organs).

I expect there are some differences in the gene expression among cell types. So, in order to analyse cell types within the same organ - let's say B Cells vs T Cells in the spleen - should I subset the dataset? Or maintaining samples from other organs can add information?

Thanks in advance!

That's addressed in the FAQs http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#if-i-have-multiple-groups-should-i-run-all-together-or-split-into-pairs-of-groups