LMGene (version 2.28.0)

transeS: Function to apply the glog transform to an expression set.

Description

For each element in the array of expression data, this function applies the glog transform y -> glog (y-alpha, lambda). If alpha is a vector, it must have one element for each column in exprs(eS).

Usage

transeS(eS, lambda, alpha)

Arguments

eS

An ExpressionSet or AffyBatch object

lambda

The parameter lambda to be used in the glog transform.

alpha

The alpha parameter(s) for the glog transform. May be a single number used for all samples, or a vector with one entry per sample.

Value

Returns an ExpressionSet or AffyBatch object with the expression matrix glog-transformed.

Details

The glog transformation of a variable y is defined as log(y + sqrt(y^2 + lambda)). Using lambda = 0 corresponds to the log transformation, up to a scale factor of 2. (Other, equivalent expressions exist for the glog transformation. See Durbin et al. (2002) and Huber et al. (2002) for futher details.)

transeS subtracts a (scalar or vector) parameter alpha prior to application of the glog transformation, resulting in the expression log(y - alpha + sqrt((y - alpha)^2 + lambda)).

The parameters lambda and alpha may be estimated using tranest.

References

Durbin, B.P., Hardin, J.S., Hawkins, D.M., and Rocke, D.M. (2002) A variance-stabilizing transformation for gene-expression microarray data, Bioinformatics, 18, S105--S110.

Huber, W., Von Heydebreck, A., Sueltmann, H., Poustka, A., and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics, 18, S96--S104.

http://dmrocke.ucdavis.edu

See Also

glog, tranest

Examples

library(LMGene)
library(Biobase)

data(sample.eS)
trsample.eS <- transeS (sample.eS, 667, 65)