Cutoff analysis results

macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq

https://macs3-project.github.io/MACS/

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Cutoff analysis results #191

Open kernco opened 7 years ago

kernco commented 7 years ago

I'm confused about the output in the cutoff_analysis.txt file generated when the --cutoff-analysis argument is used. Why are the pscore and qscore values ranging from ~10 to 0? Are these -log(pvalue) and -log(qvalue)? Also when using the macs2 command you can only specify a p-value OR a q-value, but the cutoff analysis shows peak calling results for pairs of p-value and q-values. I'm not sure how to interpret that.

flyingicedragon commented 3 years ago

@taoliu replied in another issue.

https://github.com/macs3-project/MACS/issues/312#issuecomment-528906433

Q-values are caculated from p-values.

Q-values are the name given to the adjusted p-values found using an optimised FDR approach. The FDR approach is optimised by using characteristics of the p-value distribution to produce a list of q-values.