I have a doubt about the cutoffs in DESeq2 related to padj and fold change. I initially did all my analyses using the default parameters in "results" function. Afterwards, I decided to use cutoffs of padj<=0.05 e FC>=2.0. To do so, I used the results table from those default analysis and filtered based on these cutoffs I wanted.
Later, I read again DESeq2 documentation and saw the arguments "alpha" and "lfcThreshold" in "results" function. My question is if the way I did before (to filter the results table after default analysis) was correct or I need to do all my analysis again using the arguments in results function.