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Missing filenames #1

Closed cvanderaa closed 1 year ago

cvanderaa commented 1 year ago

Dear Sabrina, @SabrinaRichter

Thank you for the the reproduction script! I am trying to reproduce your analysis, but can't figure out which input files you used for the TSCP analysis. In the Data Loading section, you set twice filename = '...'. I must admit I'm a python novice, but this looks like a placeholder rather that pointing to an actual file. Could you please tell which files you used as input. I found several files in the DIANN1.8_SingleCells_CellCycle.zip folder from the repo mentioned in the Brunner et al. 2022 paper: https://www.ebi.ac.uk/pride/archive/projects/PXD024043

Thanks in advance, Chris

SabrinaRichter commented 1 year ago

Dear Chris,

Thanks for catching this! We adjusted the PRIDE upload, you can find the used files here https://www.ebi.ac.uk/pride/archive/projects/PXD024043 in DIANN1.8_SingleCells_CellCycle.7z.

I also added two more files to this repo so that it is actually possible to run the notebook instead of just functioning as a documentation.

Best, Sabrina

cvanderaa commented 1 year ago

Thank you for taking the effort of adapting the repo and making sure the notebook can be run.

Quick question: where 20210919_DIANN_SingleCellOutput.pg_matrix_notnormalized.tsv and 0210919_DIANN_SingleCellOutput.pg_matrix_cellcyclepred.tsv generated by DIA-NN? If not, how where they generated?

AndreasDavidBrunner commented 1 year ago

Hi cvanderaa,

We analysed all data with Spectronaut and DIA-NN since reviewers asked for this comparison.

All data are deposited in the PRIDE repository as presented in the methods section of the paper. The data analysed and presented in the main paper are DIA-NN data using a hybrid library created by MSFRAGGER. All processing steps are described in depth in the methods section of the paper.

If there are any other questions left with regards to the paper, I can offer quick replies by E-Mail via abrunner@biochem.mpg.de .

Cheers Andreas-David Brunner