A question about MSstats

A question about MSstats 1214800593  2020-04-26

I want to do a DIA project, but when I use the MSstats,it report error like attachment.
please help me!
Steven Liu

Nick Shulman responded:  2020-04-26
I have never seen an error message from MSstats that looks like that with those weird characters.

Can you send us your Skyline document?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
-- Nick
1214800593 responded:  2020-04-26
Thank you so much!
The .zip file have been uploaded at https://skyline.ms/files.url.
Waiting for your reply.
Nick Shulman responded:  2020-04-26
Steven Liu,

Thank you for sending us that file.
The error message that I see is:
Error in data.frame(PROTEIN = raw.temp$Protein, PEPTIDE = raw.temp$Peptide, :
  arguments imply differing number of rows: 0, 1

I am not sure why the error message in your Skyline screenshot has invalid characters. It might be that the Immediate Window in Skyline is not handling the output from R correctly. If you could tell us more about your Windows language settings, we might be able to reproduce this problem and fix it.

I believe you are getting this error in MSstats because your dataset has only 2 replicates.

MSstats outputs a warning message for you about this:
** 753 features have 1 or 2 intensities across runs and are removed.

If you only have 2 replicates, it is not possible for MSstats to do any sort of p-value or confidence interval calculations.

You can use the Group Comparison feature in Skyline instead of MSstats. You can get to that by going to:
View > Other Grids > Group Comparisons > Add

-- Nick
1214800593 responded:  2020-04-27
As you say,the problem has been solved by importing more replicates!
MSstats can work normally now!
Thank you Nick!

--Steven Liu