getPvalues: Convenient function to compute p-values from a gene...
In ycl6/topGO-feat: Enrichment Analysis for Gene Ontology

Description Usage Arguments Value Author(s) See Also Examples

Warping function of "mt.teststat", for computing p-values of a gene expression matrix.

   getPvalues(edata, classlabel, test = "t", 
	      alternative = c("greater", "two.sided", "less")[1], genesID = NULL, 
	      correction = c("none", "Bonferroni", "Holm", "Hochberg", "SidakSS", 
			     "SidakSD", "BH", "BY")[8])

`edata`	Gene expression matrix.
`classlabel`	The phenotype of the data
`test`	Which test statistic to use
`alternative`	The alternative of the test statistic
`genesID`	if a subset of genes is provided
`correction`	Multiple testing correction procedure

An named numeric vector of p-values.

Adrian Alexa

GOKSTest, groupStats-class, getSigGroups-methods

library(ALL)
data(ALL)

## discriminate B-cell from T-cell
classLabel <- as.integer(sapply(ALL$BT, function(x) return(substr(x, 1, 1) == 'T')))

## Differentially expressed genes
geneList <- getPvalues(exprs(ALL), classlabel = classLabel,
                       alternative = "greater", correction = "BY")

hist(geneList, 50)