Does higher IDR mean less 'reproducible' or vice versa?

[Chun]

IDR package produces a output file which mimics the input narrowPeak file with additional two columns stating localIDR and globalIDR. Both localIDR and globalIDR represents -log10 IDR values. Global IDR is more informative since it is more like multiple test corrected value of local IDR, according to this post (https://groups.google.com/forum/#!topic/idr-discuss/FY2K5VKx8AQ)

So if I want to find the most reproducible peaks, should I select the peaks with higher globalIDR or lower globalIDR? In other words, Does higher IDR mean less 'reproducible' or vice versa?

Another question I have is about pvalue/qvalue in 12-col report. Is the pvalue/qvalue for the peak prediction or for IDR test? In the original individual input narrowPeak file, you have pvalue representing the peak calling confidence for each peak in each file. When you combine in idr, how do you get pvalue/qvalue for it? average the original pvalue from all inputs?

[Anshul Kundaje]

IDR package produces a output file which mimics the input narrowPeak file with additional two columns stating localIDR and globalIDR. Both localIDR and globalIDR represents -log10 IDR values. Global IDR is more informative since it is more like multiple test corrected value of local IDR, according to this post (https://groups.google.com/forum/#!topic/idr-discuss/FY2K5VKx8AQ)

So if I want to find the most reproducible peaks, should I select the peaks with higher globalIDR or lower globalIDR? In other words, Does higher IDR mean less 'reproducible' or vice versa?

IDR for reproducibility should be interpreted analogous to FDR for false discoveries. The lower the value the better the reproducibility. But note that in -log10() units the higher the value the better the reproducibility of the peak.

 

Another question I have is about pvalue/qvalue in 12-col report. Is the pvalue/qvalue for the peak prediction or for IDR test? In the original individual input narrowPeak file, you have pvalue representing the peak calling confidence for each peak in each file. When you combine in idr, how do you get pvalue/qvalue for it? average the original pvalue from all inputs?

The pvalues and qvalues are from the original peak caller. They have nothing to do with IDR. They can be used as a ranking measure for peaks to compute IDR scores but they are not the output of the IDR test.

Please note that in the most update version of our IDR package https://github.com/kundajelab/idr the IDR output will retain the pvalues, qvalues of the peaks alongside the IDR scores.

-Anshul.

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