glog: Generalized log transformation function

In LMGene: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

Description

This function transforms the input values by the generalized log function.

Usage

glog(y, lambda)

Arguments

y	A data matrix
lambda	Transformation parameter

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.)

The input matrix y may be modified prior to transformation by subtracting a constant or vector ("alpha"). The parameters lambda and alpha may be estimated from tranest.

Value

yt	A matrix of glog-transformed values

Author(s)

David Rocke and Geun-Cheol Lee

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

tranest, transeS

Examples

#library
library(Biobase)
library(LMGene)

#data
data(sample.mat)
sample.mat[1:5,1:4]

GloggedSmpd<-glog(sample.mat-50,500)
GloggedSmpd[1:5,1:4]

LMGene documentation built on April 28, 2020, 8:01 p.m.