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!
Post a Comment