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fgcz / prolfqua

Differential Expression Analysis tool box R lang package for omics data
https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.2c00441
MIT License
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Sample Rscript to process fragpipe lfqMBR outputfile #56

Closed BenSamy2020 closed 1 year ago

BenSamy2020 commented 1 year ago

Greetings,

That you for providing this opensource package. By any chance would you be able to direct me to the location where the sample RScript is to process FragPipe LFQMBR output file?

Regards, Ben

wolski commented 1 year ago

Hi Ben,

An example where the "combined_protein.tsv" produced by FragPipe is used as the input you can find here: https://wolski.github.io/prolfquabenchmark/articles/BenchmarkFragPipeProteinIonStar.html

Since FragPipe also writes "MSstats.tsv" output, you can look at this vignette. https://wolski.github.io/prolfquabenchmark/articles/BenchmarkFragPipeMSStats.html

Thanks for giving prolfqua a try. Best