| runWilcox {EMA} | R Documentation |
This function provides a convenient way to compute the wilcoxon statistics, for each row of a data frame using the multtest package. It returns the raw and adjusted pvalues for each genes as well as the significance of the genes and a quantile-quantile plot.
runWilcox(data, labels, typeFDR = "FDR-BH", q = 0.05, plot = TRUE)
data |
A matrix, a data frame, or an ExpressionSet object. Each row of 'data' (or 'exprs(data)', respectively) must correspond to a gene, and each column to a sample. |
labels |
A vector of integers corresponding to observation (column) class labels. For 2 classes, the labels must be 0 and 1. |
typeFDR |
The method to apply fo the multiple testing correction. |
q |
A numeric value specifying the pvalue threshold. |
plot |
A logical value specifying if drawing plots or not. |
A matrix with the probes ID, the statistics, the raw p-value and the adjust p-value
EMA group
mt.teststat,multiple.correction
## load data data(marty) ## filtering data ##marty <- expFilter(marty, threshold=3.5, graph=FALSE) ##Class label 0/1 marty.type.num <- ifelse(marty.type.cl=="Her2+",0,1) ## run differential analysis example.subset<-marty[1:100,] out <- runWilcox(example.subset, labels=marty.type.num, typeFDR="FDR-BH", plot=FALSE)