logitT {plw} | R Documentation

## logit-t and t-test by row

### Description

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

### Usage

    logitTTransform(pm)
    logitTStat(affy.batch,group)
    studenttTTest(x, group)

### 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

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

[Package plw version 1.4.0 Index]