Benchmarking vignettes comparing differential expression analysis methods — prolfqua, MSstats, proDA, msqrob2, limma, and DEqMS — using the IonStar and CPTAC gold-standard datasets.
Full documentation and rendered vignettes: https://prolfqua.github.io/prolfquabenchmark/
Vignettes
| Dataset | Vignette |
|---|---|
| IonStar / MaxQuant | Benchmarking normalization, aggregation and models |
| IonStar / MaxQuant | MSstats |
| IonStar / MaxQuant | proDA (LFQ intensities) |
| IonStar / MaxQuant | proDA (peptides) |
| IonStar / MaxQuant | msqrob2 |
| IonStar / MaxQuant | Robust linear model |
| IonStar / MaxQuant | Two-factor model |
| IonStar / FragPipe | combined_protein.tsv |
| IonStar / FragPipe | MSstats.tsv |
| CPTAC / MaxQuant | peptide.txt |
The inst/MyArticle/ directory contains the source for the prolfqua manuscript (paper.Rmd) and its supplement (prolfqua_supplement.Rmd), buildable via make from that directory.
Installation
remotes::install_github("wolski/prolfquabenchmark", dependencies = TRUE)