Where to find cell cycle adjusted file?

[enryH]

Hey,

thanks for the interesting work and the provided notebook. I tried to wrap my head around the study and wonder where I can find 20210919_DIANN_SingleCellOutput.pg_matrix_cellcyclepred.tsv which I assume is the "normalized data using the retention time-dependent normalization module offered by the search engine DIA-NN across cells" mentioned in the paper?

Or is it something else? I could not find it in the PRIDE archive in the DIANN1.8_SingleCells_CellCycle.zip folder.

• the unnormalized processed data in the notebook, name 20210919_DIANN_SingleCellOutput.pg_matrix_notnormalized.tsv is 20210919_DIANN_SingleCellOutput.pg_matrix.tsv in the zip file?

[fabianegli]

The answer in issue https://github.com/theislab/singlecell_proteomics/issues/1#issuecomment-1259469471 points to a zip file on PRIDE together with additional explanations about the what they contain and how they were generated.

[enryH]

Thanks! I found the files. I did not expect that files with the same name, but different file extension, contain different files. Maybe the zip file could be deleted on PRIDE as it contains the same files expect the two additional ones?

[fabianegli]

Generally, I agree it is confusing. However, I would favor a clear documentation about the used files in the README and/or Jupyter Noteook rather than plain out removing files from PRIDE.