I'm looking at identifying differentially expressed genes. I'm using Salmon, importing the quantification using tximport as outlined here. It's a simple comparison using infected and non-infected, and I've tried using three differential expression pieces of software (edgeR, DESeq2 and Limma).
However, for one of the conditions (there are only 2 reps), one rep is unfortunately a bit different from the other (actual gene expression). As a result, the number of DE genes is reduced and is making any biological interpretations challenging. To help with this, I'd like to use RUVSeq (RUVs), but I'm not entirely sure how to use the offsets correctly.
Although slightly different but related, I've looked at the offsets section of the EDASeq vignette, and from what I can see, theoretically I should be able to use the offsets as input into RUVSeq. I just don't want to calculate this incorrectly and end up interpreting the data wrong
Any ideas or suggestions would be greatly appreciated!