I have a question regarding the results of DESeq2.
With one dataset, by changing the lfcthreshold from 0 to 0.75 I found a decrease in the number of DEGs ---- from 100 to 3. DESeq gave 101 for another set of data with an lfcthreshold of 0.75 and 215 for an lfcthreshold of 0.
Why is the DEG drop more in the first case? Is it because of the variation in the read counts in the replicate samples?