I am new to proteomics analysis, so apologies if my question is silly! For context, I am working with proteome samples from the postmortem human brain for a case-control study.
Our lab generally receives an output file of Proteome Discoverer* (v2.5) from the proteomics center that we work with. From what I understand, PD perform t-tests on the normalized data, but it is a background-based t-test, so there is a weighting factor is applied that takes into account the distribution of ratios for all other proteins and/or the protein abundances themselves? As such, I am able to see an "Abundance Ratio Adj. P-Value".
My problem is that my data does not meet the assumptions for a parametric test and it has a small sample size, so the t-test is not valid (as far as I can tell, unless there is some sort of log transformation that PD does to the data before the t-test). Therefore, I would like to run a Mann-Whitney U Test. Can this be done in the PD software?
If not, how can I do this background adjustment manually such that I can run a Mann-Whitney U Test but still take into protein abundance like in PD? I do most of my stats in R in case that is relevant.
Thank you so much in advance for your help!
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