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Error #10

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Maithy15 opened this issue Apr 6, 2022 · 5 comments
Closed

Error #10

Maithy15 opened this issue Apr 6, 2022 · 5 comments
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@Maithy15
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Maithy15 commented Apr 6, 2022

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 tbaccata self-assigned this Apr 6, 2022
@tbaccata tbaccata added the help wanted Extra attention is needed label Apr 6, 2022
@tbaccata
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tbaccata commented Apr 6, 2022

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
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Maithy15 commented Apr 7, 2022

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
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tbaccata commented Apr 7, 2022

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
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Maithy15 commented Apr 7, 2022

ahh there is a mistake in the caps and small letter

Thanks for the help
Maithy

@tbaccata
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tbaccata commented Apr 7, 2022

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

@tbaccata tbaccata closed this as completed Apr 7, 2022
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