Hi,
I have a stragne problem with MSstats as an external tool.
I have comparison for a single analyte (small molecule) with stable isotope labeled standard (two conditions, 14 subjects, triplicate measurements). While a can use the "Group Comparisons" from the "View" menu, I get the following error message when trying to use Group Comparison from MSstats in the "Tools" menu:
>Error in aggregate.data.frame(mf[1L], mf[-1L], FUN = FUN, ...) :
> no rows to aggregate
The respective file is present and has data rows in it. What am I missing?
Many thanks!
Joerg |
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| Brendan MacLean responded: |
2018-01-19 08:39 |
Hi Joerg,
Your best bet will be to post this to the MSstats support board, which you can get to by clicking the red "Support Board" button on its external tool web page:
https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=MSstats
The Skyline development team does not support external tools. They are owned by third parties that integrate their work with Skyline.
Thanks for using Skyline and MSstats in your work. I know the MSstats team will be very responsive in helping you work through this.
--Brendan |
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| Nick Shulman responded: |
2018-03-02 10:44 |
Sorry about not responding to this question earlier.
MSstats does not work with small molecules. The reason for this is that the MSstats input report relies on the "PeptideModifiedSequence" column, which is blank for small molecules.
I just saw your post today on the MSstats support board. I will reply to you there too so the MSstats team will see the answer. |
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| <13763> responded: |
2018-03-05 07:45 |
Hi Nick,
many thanks, didn´t know that...
As expected it worked well when I tried with peptides. I will try to do a workaround, but I am looking forward to full small molecule support.;-)
Regards,
Joerg |
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