YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization
https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
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Why I get different p value when I exchange the queryPeak and targetPeak in enrichPeakOverlap #84

Open wkl1990 opened 6 years ago

wkl1990 commented 6 years ago

Describe you issue

I run the enrichPeakOverlap using two peak files two time with the same parameters and just exchange them (one for queryPeak and the other for targetPeak and swap them in the second run). The overlap peaks is same. However, I get the different p value (large difference) for two run. Another question, why the number of overlap peaks may be more than one of the raw peaks number?

wkl1990 commented 6 years ago

Maybe it is caused by the pool parameter. Because I set the targetPeak more than one peak file in the first run.

GuangchuangYu commented 6 years ago

yes, pls try pool=F.

For p value issue, pls use larger nPerm.

JingqunMa commented 6 years ago

I have the same issue with getting different p values when simply swap the query and target peaks. sometimes the difference is drastic. (i.e., one is significant, the other is not)