logit-t and t-test by row

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Description

Functions for the logit-t test (Lemon et al. 2003) and the ordinary t-test computed for each row of an matrix.

Usage

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Arguments

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

Details

See the definition (R-code) of each function for details.

Value

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.

Author(s)

Magnus Astrand

References

Lemon et al. (2003). A high performance test of differential gene expression for oligonucleotide arrays. Genome Biol. 2003; 4(10):R67

Examples

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# ------------------------------------------
# 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)