I am unable to run MSStats on my dataset. I am able to do it with other similar size datasets, and actually I can still do it with an older version (pre-curation) of this one, but somehow now It wont run. Here's the error message I am getting:
Error in factor(work$RUN, levels = unique(work$RUN), labels = seq(1, length(unique(work$RUN)))) :
invalid 'labels'; length 2 should be 1 or 0
Error : Can't process the data.
Error in runComparison() :
Can't finish analysis.
I also downloaded the file and tried running it on my local R MSstats implementation (on a MAC) and it works! So it is something related to how Skyline is formatting the output for the one installed there.