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error running make_se_from_files using diann pg matrix #14
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@jflucier Is your DIA-NN input file generated by running FragPipe? |
Also, which version you are using? |
Hi
No, I run DIANN using command line on a linux cluster. Here is the command I use:
I use DIANN v1.8.1 installed inside a singularity container built using docker image. Thank you again for your help |
I was asking about the version of FragpipeAnalystR. I believe FragPipe doesn't generate report with such issue. We are willing to support DIA-NN report more but currently we don't support that yet. If you are willing to share your file, you can send it to me through email [email protected] |
The FragPipeAnalystR version installed is 0.1.7 I will send you my analysis file directly to the provided email Thanks again! |
Hello, I manage to get this working by filtering pg report using only proteotypic proteins groups (those without ; in protein_group name). Here is the command I used to filter:
Afterwards, the following command run with success:
|
Hi,
When pass my DIANN result file to the
make_se_from_files
function, it returns the following error:I have trace back by executing line by line the
make_se_from_files
function and found where the error happens. It happens in themake_unique
function that returns duplicates. If I inspect the returnedproteins_unique
object, the returned ID is truncated in the case where proteins groups are composed of multiple proteins. For example:Diann protein group: ID
A0A075B5M4: A0A075B5M4
A0A075B5M4;A0A0A6YYE7: A0A075B5M4
Would it be ok to prefilter diann results to remove all lines where I see a group of more then 1 protein like A0A075B5M4;A0A0A6YYE7 or it will bias results.
Thank you in advance for your help,
JF
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