diffAna {DAPAR} | R Documentation |
limma
)Performs a differential analysis on an MSnSet
object,
based on limma
functions.
diffAna(qData, design)
qData |
A dataframe that contains quantitative data. |
design |
The design matrix as described in the limma package documentation |
A dataframe with the p-value and log(Fold Change) associated to each element (peptide/protein)
Florence Combes, Samuel Wieczorek
require(DAPARdata) data(Exp1_R25_pept) qData <- Biobase::exprs(Exp1_R25_pept[1:1000]) design <- cbind(cond1=1, cond2 = rep(0,nrow(Biobase::pData(Exp1_R25_pept[1:1000])))) rownames(design) <- rownames(Biobase::pData(Exp1_R25_pept[1:1000])) labels <- Biobase::pData(Exp1_R25_pept[1:1000])[,"Label"] indices <- getIndicesConditions(labels, "25fmol", "10fmol") design[indices$iCond2,2] <- 1 diffAna(qData, design)