Error about amica

[tbaccata]

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]

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]

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]

ahh there is a mistake in the caps and small letter

Thanks for the help
Maithy

[tbaccata]

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