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tbaccata / amica

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
GNU General Public License v3.0
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Custom file upload error #11

Closed Maithy15 closed 2 years ago

Maithy15 commented 2 years ago

Hi Sebastian,

I have a custom output file from DIA-NN. It seems to be getting uploaded successfully but when I press analyze it says no data uploaded. I have attached the files here. Could you please tell me what could be the problem?

Thanks Maithy

image amica_groups.txt amica_specification.txt Pel_Amica_Example.txt amica_expt.txt

tbaccata commented 2 years ago

Hi Maithy,

the ... in the Pattern column of the example specification file is just be a placeholder, columns that are missing in your data must not be declared in the specification file, which throws an error.

The file Pel_Amica_Example.txt contains 48 Intensity columns, but only 47 are declared in amica_expt.txt. The 2nd sample in Pel_Amica_Example.txt M08_R1_Pel is missing in amica_expt.txt, amica fails to succesfully assign all samples to groups.

I've added the sample M08_R1_Pel to the group R1_Pel at the 2nd position of the file design.txt (hope that is correct). design.txt

And I've attached you an appropriate specfication file. specification.txt

Then it should work.

Best, Sebastian

Maithy15 commented 2 years ago

Hi Sebastian,

M08 was a mistake in the example file.

Thanks for the specification.txt

When I upload the example file it works fine but when I upload the full file it says no data uploaded again.

Thanks Maithy

Maithy15 commented 2 years ago

I will try a different file and let you know later.

Maithy15 commented 2 years ago

Hi Sebastian,

I think there was some problem with the previous dataset I was using. It works now.

Thanks for the great app Maithy