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jajclement / hotSSDS

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Macs pvalue or qvalue #11

Open andpet0101 opened 1 year ago

andpet0101 commented 1 year ago

Hi,

I noticed that with the mm10.config MACS uses the pvalue instead of the (multiple-testing-corrected) qvalue. Consequently, we get much more peaks but many of them will be false-positive. Now I was wondering: Should MACS by default be run with the qvalue threshold? Is there a situation where you would use the pvalue threshold?

For now we will be switching to qvalue...

Thanks,

Andreas