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CollasLab / edd

Enriched Domain Detector for ChIP-seq data
https://pypi.python.org/pypi/edd
MIT License
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FDR specification #7

Closed yeminlan closed 7 years ago

yeminlan commented 7 years ago

We tested two similar runs with different FDR specification, and it turns out the "--fdr" parameter ranges from 0-100 instead of 0-1.

[log.txt file from run1]: NOTICE: eddlib.algorithm.max_segments: got 72 peaks with qvalue below 1.00. From 215 possible. [log.txt file from run2]: NOTICE: eddlib.algorithm.max_segments: got 215 peaks with qvalue below 100.00. From 215 possible.

Maybe it's because we were using python package "statsmodels" version 0.6.1 instead of the most most recent version. We haven't tried that yet.

yeminlan commented 7 years ago

Hmm...that might not be the case since we tried fdr==1.01 and got all 215 peaks. So it must be that the FDR cutoff does not include the specified value itself, that's fine.