Harald Barsnes

Hi Sameh, The GO Analysis tab in PeptideShaker uses so-called Gene Ontology Enrichment Analysis (GOEA). GOEA analyzes the frequencies of GO terms in your dataset and compares these to the...

Hi, I'm afraid this is something you would have to implement yourself as there is not yet any support for merging the reports. We are considering implementing such a feature,...

Hi Thys, Thanks for telling us about this. If I diff the two files (they are just text files in the json format), I see a difference in the maxMassDeviation...

Hi again, The results when using the GUI or the CLI option to create a parameter file ought to be identical. However, from your example files I've detected some very...

If the first command line works fine, I would suggest merging the two into one command line: java -Xmx96G -cp PeptideShaker-2.0.33/PeptideShaker-2.0.33.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -reference "Reference_name" -identification_files "files.zip" -zip "PeptideShaker.zip" -out "PeptideShaker.psdb"\...

> Do you have any idea why I am encountering “ClassCastException” error? Is it related to the fasta database or mgf file, etc.? I'm afraid this is a known issue...

I assume the pull request your referring to is this one: https://github.com/compomics/peptide-shaker/pull/207? As you can see it was accepted and merged into the master branch. And the release are always...

> The #207 I saw had the exact same stack trace, so in theory it should have been caught by the "catch" clause at line 361... That's in theory, perhaps...

Good point! Any suggestions for what we ought to use instead of comma? As we still want the text to be easy to read.

Hi Tim, Now that you mentioned it, aren't all our default text exports tab based, i.e. tsv files and not csv files? Which means that this issue only occurs if...