I am attempting to run an MsStats analysis on some proteomics data that I have ran through maxquant previously. When I run the MsStats on default it goes no problem. However, I receive the error listed above when I try to have it compare across treatment groups. Does anyone have any suggestions on how to clear this error for my proteomics data to have a group comparison in MsStats?
Hi @lindsey
In general: if a tools works on a single group of data in isolation but fails when running it with multiple groups – there is either a problem with one of the other groups (you could test this) OR a problem with how those datasets are “connected” through a common key or attribute.
We have tutorials for the tool here that may help. → GTN Tutorials for MSstats: statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry. You can also find this at the bottom of the tool form (scroll down).
Then, for troubleshooting the specific error you are getting, click into the i-icon for your red error dataset. Down in the job logs – expand the sections to review. The logs reported here are directly from the underlying tool. You can search with that error to learn what it means – sometimes at this site if it happened to come up before – but you can also try a general search, too.
This is at least part of your error, and it suggests that you have an empty value that you tried to perform a mathematical function against.
In max(common$n_common) : no non-missing arguments to max;
An “empty” value is a blank or NULL value, not a number with a 0 value. Whether that is a value in your input file, or something that you calculated during the runtime, can’t be determined from this message alone but maybe this helps you anyway?
Thanks and let us know how this works out! 