Error during conversion from MaxQuant to MSStat format

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Giulio.F

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Feb 22, 2022, 1:32:34 PM2/22/22
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Hi, 

I was just looking into your package and I was trying to analyse a set of LFQ data. But when converting my data into a MSStat format it gives me this error. I searched but I have not found anything similar. 

What am I doing wrong? 


INFO  [2022-02-22 19:20:21] ** Raw data from MaxQuant imported successfully.
INFO  [2022-02-22 19:20:21] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
Error in merge.data.table(mq_input, unique(mq_pg[, list(uniquefromProteinGroups = ProteinIDs,  :
  Elements listed in `by` must be valid column names in x and y
In addition: Warning message:
In merge.data.table(mq_input, unique(mq_pg[, list(uniquefromProteinGroups = ProteinIDs,  :
  You are trying to join data.tables where 'y' argument is 0 columns data.table.

Mateusz Staniak

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Feb 22, 2022, 1:36:39 PM2/22/22
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Hi,


just looking at that error message: is there a ProteinIDs in your protein groups file?


Kind regards,
Mateusz

Mateusz Staniak

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Feb 22, 2022, 1:38:37 PM2/22/22
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Correction: id column and ProteinDs column



Kind regards,
Mateusz
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Giulio.F

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Feb 22, 2022, 2:07:54 PM2/22/22
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Yest, both columns are present in the file.

Best, 

Giulio

Mateusz Staniak

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Feb 22, 2022, 2:55:18 PM2/22/22
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Just to make sure: lowercase "id", "ProteinIDs"?
Additional question: is there a "ProteingroupIDs" column in evidence file?


Kind regards
Mateusz

Giulio.F

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Feb 22, 2022, 3:09:35 PM2/22/22
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Yes to all questions, id (lowercase) and ProteinIDs are present. And yes, in the evidence file there is a Protein Group ids column.

Mateusz Staniak

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Feb 22, 2022, 3:14:30 PM2/22/22
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If it written exactly as ProteingroupIDs (or the same with spaces/dots/etc, it's the letter case that matters here), means something went wrong earlier.
Can you please share a small subset of your data (it can be anonymized by changing protein/condition/etc labels) that reproduces the error?


Kind regards,
Mateusz

Giulio.F

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Feb 22, 2022, 3:36:17 PM2/22/22
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I am really really dumb as I completely forgot that I needed to add TRUE to header in this case. Really sorry, very long day.
Thank you for your kind attention and quick response time. So sorry to bother you.


Best, 

Giulio

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