Hi, I have been using "csaw" to compare ChIP-Seq samples from two conditions. However, I have 2 samples in one condition, and 3 samples in the other condition, no control (input). I'm concerned with the independent filtering step done by filterWindows, which does independent filtering by averaging the signal within each window across all ChIP-Seq samples ( in this case 5 samples) and compared that to the input signal. As I can think of, bindings that only present in the condition with fewer samples are less likely to be kept, or it has to be at a higher intensity in order to be kept, and which may lead to more false negatives because they are not even considered in the DB step downstream.
For example, the normalized read count in my samples are 15, 15, 0,0,0, the average is 6. Let's say the global background is 2, and desired FC is 3. Then for the above window, FC = 6/2 = 3, which just meets the criteria. However, if there is another window that only has reads from the other condition, and read counts are like 0,0,10,10,10, average=30/5=6, FC:6/2=3, also pass the criteria. However, the actual signal is weaker compared to the first scenario. Does anyone have the same concern, or have idea how to work around this issue? Thank you for your suggestions!