Witold Wolski

Dear Jim, Thanks, But can't get `package_coverage( type="example" )` Still same problem "could not find function xyz" all over the place. Only way to get it working is to call...

Just tried it: a) will need a grpc build with the same compiler as used by Rtools - mingw so I did some searching and the windows prebuild binary based...

Updated Makevars.win to: ``` PKG_CPPFLAGS=-D_WIN32_WINNT=0x600 -IC:/msys64/mingw64/include PKG_LIBS=-LC:/msys64/mingw64/lib -lgrpc -lgpr ``` And it seems to build. There are now in the src folder : ``` $ ls *.o *.dll client.o grpc.dll*...

Dear @vdemichev Although I specify the "\report-lib.tsv" in the GUI, and the options seem to be passed to the diann.exe ``` diann.exe --lib "" --threads 16 --verbose 1 --out "D:\WEW_o29132_\BENCHMARKING\report.tsv"...

@Arthfael Running the command ``` diann.exe --lib "D:\WEW_o29132_\BENCHMARKING\report-lib.predicted.speclib" --threads 16 --verbose 1 --out "D:\WEW_o29132_\BENCHMARKING\report.tsv" --qvalue 0.01 --matrices --out-lib "D:\WEW_o29132_\BENCHMARKING\report-lib.tsv" --gen-spec-lib --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal ``` On the generated speclib...

Hi Marc, I could share the file with you but you can easily reproduce the error by first creating a pepXml from Peptideshaker (1.13.6) by running Export -> Follow up...

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...

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

possible replace with -> get LOD -> impute -> build models with lm -> when computing contrasts update degrees of freedom etc.

- update of statistics when computing interaction is still needed - see vignette posthoc InteractionAnalysis in [prolfquapp](https://github.com/prolfqua/prolfquapp). - https://github.com/prolfqua/prolfquapp/blob/master/vignettes/PostHocInteractionAnalysis.Rmd