logitT (version 1.30.0)

logitTAffy: Testing for differential gene expression using the Logit-t algorithm

Description

This function takes an instance of AffyBatch and calculates t-statistics for tests of differential gene expression for oligonucleotide arrays using the Logit-t algorithm.

Usage

logitTAffy(object, group)

Arguments

object

an instance of AffyBatch

group

a vector specifying the group label for each array

Value

• A named vector containing the t-statistics for each probe set for each array.

Details

For more details see the package vignette.

References

William J Lemon, Sandya Liyanarachchi and Ming You (2003). A high performance test of differential gene expression for oligonucleotide arrays. Genome Biology 2003, 4:R67. http://genomebiology.com/2003/4/10/R67.

See Also

AffyBatch

Examples

if(require(SpikeInSubset)){
library(SpikeInSubset)
data(spikein95)
logitTex<-logitTAffy(spikein95, group=c("A","A","A","B","B","B"))
logitTex[1:10]                                                              # extract t-statistics for first ten probe sets
logitTex[grep("AFFX-BioB-5_at",names(logitTex))]                         # extract t-statistics for specific probe set
pvals<-(1-pt(abs(logitTex),df=4))*2                                         # calculate two-sided p-values
signifgenes<-names(logitTex)[pvals<0.01]                                    # find significant probe sets at 0.01 significance level
}else{
stop("Please install the SpikeInSubset package to run the example.")
}