Good morning,

We have been doing multiple trials in our lab to figure out how DESeq2 works, using a bulk RNAseq dataset. We got clear that the results() function uses a reinterpretation of Benjamini-Hochberg method (FDR) for getting the adjusted p value, as it was shown in the video:

https://www.youtube.com/watch?v=921IgQ6T6_4

We would like to ask why this simplification of BH works, as it no longer needs for a FDR cutoff. We are also confused about the role of the 'alpha' argument in the independent filtering. Thank you very much in advance!