Resampling of microarray expression values and test for differential expression.

Description

The function uses a 50% jackknife resampling to calculate a pseudo-replicate of the expression matrix. The resampled expression values are used thereupon to calculate p-values for the differential expression between the given groups. Only two-group comparisons are allowed for the perfomed t-test.

Usage

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resamplingPvalues(exprMat, groups, alternative = c("two.sided", "less", "greater"), resampleMat=FALSE)

Arguments

exprMat

Matrix with microarray expression values.

groups

Factors for two groups that are tested for differential expression.

alternative

Testing alternatives for the t-test: "two.sided", "less" or "greater".

resampleMat

Boolean value, whether to retrieve the matrix of jacknife resamples or not.

Value

A result list is returned, consisting of:

p.values

VNumerical vector of p-values.

resampleMat

Matrix of resampled expression values.

Author(s)

Daniela Beisser

Examples

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library(ALL)
data(ALL)
mat <- exprs(ALL)
groups <- factor(c(rep("A", 64), rep("B", 64)))
results <- resamplingPvalues(mat, groups, alternative="greater")

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