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pFindStudio / pGlyco2

pGlyco is a software tool dedicated for the analysis of intact glycopeptides/glycoproteins using mass spectrometry.
http://pfind.ict.ac.cn/software/pGlyco/
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FDR Estimation #35

Open mobiusklein opened 4 years ago

mobiusklein commented 4 years ago

I noticed that the results from running pGlyco2.1 on the data from https://www.nature.com/articles/s41467-017-00535-2 are different from the published results. The actual match scores are the same, but the FDRs are different. I used as similar parameters as possible to those described in the publication. I also noticed the FDR executables are different sizes between 2.0 and 2.1. Did the algorithm change?

jalew188 commented 4 years ago

@mobiusklein Yes, we still used FMM when estimating FDRs, but the details of the algorithm has been changed.

mobiusklein commented 4 years ago

Can you disclose the changes, or will they be published soon?

I am trying to benchmark an alternative scoring function against the published one, but can't do a direct comparison without using the same FDR estimation method.

jalew188 commented 4 years ago

@mobiusklein Old version had a potential dividing zero bug, it was keeping fixed from about two years ago, so we may not change it back now. I may provide a similar version, which is of course not exactly the same.