A simple question. Would you use different q-value thresholds for different peak detections in a dataset?
The chip-seq experiments all have the same input, I am performing the peak detection with macs2. I would rather use the same q-value for all experiments but since some are more noisy than others, would it be wrong to use a less stringeant q-value for those? Would you say that would be "artificially" improving the detection?