MSstats (version 2.4.0)

testResultOneComparison: Significance testing result of one comparison between two groups

Description

Consider quantitative data (i.e. QuantData) from yeast study with ten time points of interests, three biological replicates, and no technical replicates. It is a time-course experiment, and we attempt to compare differential abundance between time 1 and 7 in a set of targeted proteins. In this label-based SRM experiment, we recommend the fitted model with expanded scope of technical replication (i.e. labeled=TRUE, scopeOfTechReplication="expanded" as default).

Usage

testResultOneComparison

Details

The testing result contains variable of Protein, Comparison(Label), log2 fold change(logFC), standard error (SE), T values (Tvalue), degree of freedom (DF), raw p-values (pvalue), adjusted p-values based on Benjamini and Hochberg method to collect multiple testing issue and further control false discovery rate (adj.pvalue).

References

Ching-Yun Chang, Paola Picotti, Ruth Huttenhain, Viola Heinzelmann-Schwarz, Marko Jovanovic, Ruedi Aebersold, Olga Vitek. Protein significance analysis in selected reaction monitoring (SRM) measurements. Molecular & Cellular Proteomics, 11:M111.014662, 2012.

Examples

comparison<-matrix(c(-1,0,0,0,0,0,1,0,0,0),nrow=1)
row.names(comparison)<-"T7-T1"

testResultOneComparison<-groupComparison(contrast.matrix=comparison,data=QuantData)

testResultOneComparison$ComparisonResult