Hi,
in the benchmark output, we can find a lot of proportions relative to the output of the PolySTest such as:
propDiffRegPepWrong0.01.FDR_PolySTest 2 vs 1
propDiffRegPepWrong0.05.FDR_PolySTest 2 vs 1
propDiffRegWrongIDProt0.01.FDR_PolySTest 2 vs 1
propDiffRegWrongIDProt0.05.FDR_PolySTest 2 vs 1
tFDRPep0.01.FDR_limma 2 vs 1.tFDR
tFDRPep0.05.FDR_limma 2 vs 1.tFDR
tFDRProt0.01.FDR_PolySTest 2 vs 1.tFDR
tFDRProt0.05.FDR_PolySTest 2 vs 1.tFDR
tprPep0.01.FDR_limma 2 vs 1.TPR
tprPep0.05.FDR_limma 2 vs 1.TPR
tprProt0.01.FDR_PolySTest 2 vs 1.TPR
tprProt0.05.FDR_PolySTest 2 vs 1.TPR
I would really like to also have the total number of hits at the statistical FDR thresholds 0.01 and 0.05. This would be useful to put these proportions in perspective.
Hi,
in the benchmark output, we can find a lot of proportions relative to the output of the PolySTest such as:
propDiffRegPepWrong0.01.FDR_PolySTest 2 vs 1
propDiffRegPepWrong0.05.FDR_PolySTest 2 vs 1
propDiffRegWrongIDProt0.01.FDR_PolySTest 2 vs 1
propDiffRegWrongIDProt0.05.FDR_PolySTest 2 vs 1
tFDRPep0.01.FDR_limma 2 vs 1.tFDR
tFDRPep0.05.FDR_limma 2 vs 1.tFDR
tFDRProt0.01.FDR_PolySTest 2 vs 1.tFDR
tFDRProt0.05.FDR_PolySTest 2 vs 1.tFDR
tprPep0.01.FDR_limma 2 vs 1.TPR
tprPep0.05.FDR_limma 2 vs 1.TPR
tprProt0.01.FDR_PolySTest 2 vs 1.TPR
tprProt0.05.FDR_PolySTest 2 vs 1.TPR
I would really like to also have the total number of hits at the statistical FDR thresholds 0.01 and 0.05. This would be useful to put these proportions in perspective.