I performed a DeSeq2 analysis and after I performed the lfcshrinkage command, I obtained very small log2fold changes for some of my results. As a consequence, my enhanced volcano plot looks very weird.
For explaining my approach: I'm using TCGA-ovarian HT-Seq counts downloaded from the GDC Bioportal, Because there is a high amount of genes with 0s, I set the
keep <- rowSums(counts(dds)) >= 1000 to a 1000 as seen and then continued with my analysis. After performing lfcshrinkage I obtained the following volcano plot.
Now I'm trying to figure out if something is wrong with my data or what is the reason for this weird looking volcano plot.
Has anybody obtained similar results like this?
Thank you very much for any help