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ococrook / hdxstats

hdxstats: An R-package for statistical analysis of hydrogen deuterium exchange mass-spectrometry data.
Apache License 2.0
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hdxdifference p-value signs #43

Closed nlgittens closed 1 year ago

nlgittens commented 1 year ago

Putting this as placeholder, as I don't have a dataset I can share with you. Essentially, I have quite a large block of peptides in a protein all of which are protected at all timepoints, yet the difference plot is assigning most as +ve (deprotecting), along with some -ve residues. I don't think that this is just because of overlapping peptides. p-values are identical as to when computeAverageMap is used, I just can't rationalise the sign at all; it would be useful to parse through this

ococrook commented 1 year ago

The sign comes from the raw uptake data what are you're inputs to the function?