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License: MIT License
Hi @klevdiamanti,
first of all thank you for providing the code for the Mass-Spec analysis. I was trying to execute it but ran into an error:
tmp.azpid <- unique.gene.id(azpid.index_ = dia$index$AZpID)
Error in file(file, "rt") : cannot open the connection
which ultimately comes from the file gene.id.file <- "../data/gsea_files/all.gene.ids.txt"
not being present in the repo
https://github.com/klevdiamanti/multitissue_ms_proteomics/blob/main/R/ms_proteomics_pipeline.Rmd#L60
Could you please upload it?
A unrelated question is that the sample names in proteomics_random.xlsx
and covars_random.xlsx
are named rand* which is not the same format supplied in the supp matherials of the paper. Are these the same samples and are the intensity values those used in the papers?
Thank you!
António
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