Error when running FragPipe-analyst

[Lab123-prog]

**- log_2024-09-16_18-54-51.txt

Upload your log file** (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

- Describe the issue or question:

Cannot work with the FragPipe Analyst

Once the 2 files were added and press RUN, the above errors were generated.

Can you please let me know how I can deal with this situation.

Thank you

[hsiaoyi0504]

@Lab123-prog You might need to annotate the dataset to use FragPipe-Analyst. Could you share your experiment_annotation.tsv file?

[hsiaoyi0504]

Meanwhile, it looks like you upload combined_peptide.tsv rather than combined_protein.tsv file that required based on your configuration.

[Lab123-prog]

thank you so much, I will try it out

[Lab123-prog]

Sorry I still could not get it work.

[hsiaoyi0504]

Please post your experiment_annotation.tsv file. You need to have more than one sample for each condition, or differential expression might not work.

[Lab123-prog]

Please find the experimental annotation file experiment_annotation.zip

[Lab123-prog]

Hi I would like to know whether the fragpipe data- the combined protein. tsv file we obtain is normalized or not .

[hsiaoyi0504]

It's not normalized before uploaded into FragPipe-Analyst

[hsiaoyi0504]

@Lab123-prog I checked your experiment_annotation.tsv As I mentioned, you need to have a least two samples for each condition or any DE might give the error.

[hsiaoyi0504]

Closed since no further response.