Thursday, July 15, 2021

Black sheep -- How to handle proteins with extreme ratios (R/Python)!


It would be super convenient if every protein that is differential in your model would fit nicely into your volcano plot in such a way that it is clearly differential without messing up your nice visualization.

However, sometimes get a whole list of proteins that say something like 100 because your software default is that is the maximum fold-change to report. How do you deal with those? Do you look at each one manually to see if it is a 112-fold change? Or do you wonder if you should have used imputation or something so you didn't have as many missing values (even if you divide by a quan value that is made up)? 

Black sheep is for the more serious informatics mass spectrometrists, maybe, but it is flexibly provided in both R and through Conda with really clear documentation. The test cases are really smart, including a phosphopeptide data set! 

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