Tech. replicates issue after running the dataProcess function

[Ayman REFFAI]

Hi everyone,

When running the dataProcess function of MSstats, I receive an INFO message indicating 41 runs and 41 bioreplicates (samples), as well as one tech.replicate (please
see screenshot) even though I did not include any technical replicates so it should be 0? I have double-checked my proteinGroups table, evidence, and annotation table
but cannot find where the issue is coming from.

Quick description of my data :
I have 21 samples (control condition) with 6 fractions for each sample and 41 samples (disease condition) with no fractions. Both conditions don't have any technical
replicates.
In the annotation table, I have used "1" in the fraction column for the disease samples that don't have fractions (please see screenshot). When | used "O" and "NA'
instead of "1", I got an error stopping the dataProcess function from running completely.

Has anyone experienced this issue previously?
Could you please explain how the tech.replicate feature works within the dataProcess function?

Thanks
Ayman

[Mateusz Staniak]

Hi,

thanks for reporting the issue, can I see the annotation? Must a rare issue with counting replicates or something wrong there. 

We count them as round(NumRuns / (NumBioReplicates * NumFractions), so 1 is the right number IIRC (and it means there were no actual technical replicates), I would like to look into that 0 count in control group, but I need to see the annotation. It can be anonymized by changing biorep/run/condition (etc) labels. I would also check if your way of labeling fractions is what we expect.

Kind regards,

Mateusz