logitTAffy {logitT} | R Documentation |
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.
logitTAffy(object, group)
object |
an instance of AffyBatch |
group |
a vector specifying the group label for each array |
For more details see the package vignette.
A named vector containing the t-statistics for each probe set for each array.
Tobias Guennel tguennel@vcu.edu
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.
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.") }