I'm using DESeq2 for DE analysis.
I found in the "Beginner's guide to the "DESeq2" that it's possible to perform both default independent filtering (which uses mean of normalized counts as a filter statistics) and independent filtering with other filters, such as filter=rv. Could you please explain me this last filter? Is it a filter about variance? are we speaking about gene variance within the same group?
I applied both default independent filtering and independent filtering with filter=rv on my dataset and whereas in the first case I had no improvement in the number of statistically significant DE genes, in the second case I had more DE genes.
Could it be that this difference be due to a too low number of samples in my dataset, therefore a high variance within groups. therefore more powerful filtering using variance?
Thanks a lot for your help!