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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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integrate proDA #25

Open wolski opened 2 years ago

wolski commented 2 years ago

Add proDA as a further modeling option in prolfqua.

wolski commented 2 years ago

In proDA you specify the contrasts differently than in prolfqua, But I think I can work around it using run_wald_parameter_test (currently private function). seems that the second argument it takes is:

                 (Intercept) Treatmentplacebo
Treatment16mg              1                0
Treatmentplacebo           1                1
16mgvsPlacebo              0               -1
wolski commented 8 months ago

It seems that proDA now has a contrast interface similar to that of prolfqua https://bioconductor.org/packages/release/bioc/vignettes/proDA/inst/doc/Introduction.html