I am analyzing a dataset that includes both gene and transposable element raw counts.
I am only interested in analyzing the differential expression of TEs, but still need to create and normalize the entire dataset. For the DE analysis itself it is not a major problem, because I can retrieve the results and filter out the genes. However, I was interested in plotting the variance-stabilized transformation of the data (or the rlog) and the PCA for the TEs only, ignoring the genes.
Is there a way to do this directly in DeSeq2?
I was thinking of providing an additional feature data column specifying "gene" or "TE", but then I don't know if it is possible post-normalization to use only the "TE" subset to make transformations and lfcShrink.
Thank you so much