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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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Error #10

Closed Maithy15 closed 2 years ago

Maithy15 commented 2 years ago

Hi I am trying to analyse my data from MQ and getting the following error "error in limma Error in names(x) <- value: 'names' attribute [2] must be the same length as the vector [0]" could you please tell me what the problem could be?

Also, the example files are in .csv format and Amica asks for tsv files. Is it possible to change that?

tbaccata commented 2 years ago

Hey!

Thanks for reporting, so far I haven't encountered this error message. Do you mind sharing a minimal example of your files for me to reproduce the error?

Regarding the example files, they are tab-separated, but have an unfortunate file extension. I will have a look at that.

Best, Sebastian

Maithy15 commented 2 years ago

Hi,

Please find the example protein groups file as well as the Amica expt. and grouping files.

Thanks Maithy

proteinGroups_amica.txt amica_Expt.txt amica_Groups.txt

tbaccata commented 2 years ago

Hi Maithy,

the groups CQStr and CQUnStr in amica_Groups.txt are not defined in the experimental design amica_Expt.txt. This should be changed to the defined groups CQSTR and CQUnSTR, then it works.

There should be an informative error message in such cases, that for whatever reason is not displayed, I'll look into this.

Best, Sebastian

Maithy15 commented 2 years ago

ahh there is a mistake in the caps and small letter

Thanks for the help Maithy

tbaccata commented 2 years ago

line 232/233 in R/server/upload.R should be changed from

if (!is.null(reacValues$expDesign) &
          length(grep(elem, reacValues$expDesign)) < 1)

to 

if (!is.null(reacValues$expDesign$groups) &
          length(grep(elem, reacValues$expDesign)) < 1)

and the user gets an appropriate error message.

Best, Sebastian