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baynec2 / mspms

R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data
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Icelogo n #23

Closed baynec2 closed 3 weeks ago

baynec2 commented 4 weeks ago

Icelogo n seems to vary by ~1 on the same set of cleavage sequences sometimes.

Investigate and fix.

baynec2 commented 3 weeks ago

This is controllable by set.seed() and directly results from the imputation.

The imputation value for a given peptide can vary just enough to knock a peptide out of the alpha denoting statistical significance if it was right on the threshold. This happens at the level of the t-test, which can then subsequently influence the statistics used to determine the significance of the AAs at each position in the icelogo.

The differences we see due to this are very small, which is why this only has a minor effect on the data and virtually no impact on the interpretation for cases where the n is large enough to make a valid conclusion.

no changes are needed. Use set.seed() if you need numbers to be consistent across multiple mspms::mspms() calls.