I'm revisiting some stats from an old MRM project (2014). We uses MSstats with the help of the lab performing the proteomics work at the time, I have the R script and have updated it to get it working, however I think some of the defaults are different now and I can't reproduce the results in R.
Is there any major differences than in skyline that I'm missing? Or differences in the dataprocess function?
- First, I recommend to check the version of MSstats you used. MSstats has big changes last couple of years. If you want to reproduce the results, you have to use the same version of MSstats.
- If you means, 'group comparison' option in Skyline, there are several major difference, like no imputation, different protein summarization and inference. If you means, 'MSstats external tool' in Skyline, it is the same as MSstats package.
- User manual at msstats.org(http://msstats.org/msstats-2/) show the options in dataProcess function for current version.
Hope to help.