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statisticalbiotechnology / triqler

The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code
Apache License 2.0
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Protein id PEPs are all 1.0 on OS X #6

Closed MatthewThe closed 5 years ago

MatthewThe commented 5 years ago

Using triqler on the example files in the repository on OS X, all but one of the protein_id_posterior_error are 1.0. All other OSs seem to be working properly at the moment.

MatthewThe commented 5 years ago

There seem to be some rounding differences between OS X and the other platforms which caused the different behavior. However, the underlying problem was the instability of the protein id PEP calculation where the logistic regression with IRLS did not converge due to bad scaling on the scoring axis. By adding a logarithm to the protein score, this has now been resolved.

As a side note, the run_test.sh still fails on OS X due to the aforementioned rounding differences. However, when running a diff between the result files, the differences turn out to be miniscule (two proteins receive quant differences in the order of 1e-5).