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bigbio / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://quantms.org
MIT License
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quantms-utils and mokapot error #377

Closed ypriverol closed 1 month ago

ypriverol commented 4 months ago

Description of the bug

The current ms2rescore supports two algorithms for rescoring mokapot and percolator. However, mokapot has a bug that looks like is related with the version of numpy. For now, the algorithm will be disabled until we find out a solution. Here is the link to the error in quantms-utils:

https://github.com/bigbio/quantms-utils/actions/runs/9281290285/job/25537018247?pr=6

Command used and terminal output

No response

Relevant files

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System information

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jpfeuffer commented 1 month ago

Looks more like a numeric instability in some matrix decomposition/inversion. Could be related to a numpy version but probably in any version it would be close to numerically unstable.

Maybe the test data is too small? Many values close to zero or close to each other?