logitT {plw} | R Documentation |
Functions for the logit-t test (Lemon et al. 2003) and the ordinary t-test computed for each row of an matrix.
logitTTransform(pm) logitTStat(affy.batch,group) studenttTTest(x, group)
pm |
A matrix of Pm intensities |
affy.batch |
An AffyBatch object |
group |
A group indicator vector, should have values 1 and 2 only. |
x |
A matrix |
See the definition (R-code) of each function for details.
logitTTransform returns a matrix
logitTStat returns a vector with the logit-t statistic for each probe set.
studenttTTest returns a vector with t-statistic for each row of x.
Magnus Astrand
Lemon et al. (2003). A high performance test of differential gene expression for oligonucleotide arrays. Genome Biol. 2003; 4(10):R67
# ------------------------------------------ # Example analyzing the 6 arrays in the # AffySpikeU95Subset data set # Loading the data data(AffySpikeU95Subset) # Vector with groups assignment group<-factor(rep(1:2,each=3)) # logit-T statistic logitT<-logitTStat(AffySpikeU95Subset, as.numeric(group)) # Computing RMA expression index data.rma<-exprs(rma(AffySpikeU95Subset)) # Ordinary t-test by row/gene studentT<-studenttTTest(data.rma, as.numeric(group)) # Comparing genes ranked top-20 logitTTop20 <- rank(-abs(logitT)) < 21 studentTTop20<- rank(-abs(studentT)) < 21 table(logitTTop20,studentTTop20)