tranest2 {LMGene}R Documentation

Glog transformation parameter estimation function 2

Description

A sub-function of tranest which search the best parameters for glog transformation.

Usage

tranest2(eS, starting = FALSE, lambda = 1000, alpha = 0, gradtol = 0.001, lowessnorm, method=1, model=NULL)

Arguments

eS Array data. must be exprSet type.
starting TRUE, if the given initial parameter values are used
lambda Initial parameter value for lambda
alpha Initial parameter value for alpha
gradtol a positive scalar giving the tolerance at which the scaled gradient is considered close enough to zero to terminate the algorithm
lowessnorm TRUE, if lowess method is going to be used
method Set optimization method; default is modified Gauss-Newton (nlm). See tranest.
model Model in terms of vlist which is compared to transformed expression data. See tranest.

Details

The input argument, eS, must be exprSet type from Biobase package. If you have a matrix data and information about the considered factors, then you can use neweS to conver the data into exprSet. Please see neweS in more detail. 'model' is an optional character string, constructed like the right-hand side of a formula for lm. It specifies which of the variables in the exprSet will be used in the model and whether interaction terms will be included. If model=NULL, it uses all variables from the exprSet without interactions. Be careful of using interaction terms with factors: this often leads to overfitting, which will yield an error.

Value

tranpar A numeric vector containing the best parameter for 'lambda' and 'alpha'

Author(s)

David Rocke and Geun-Cheol Lee

References

B. Durbin and D.M. Rocke, (2003) Estimation of Transformation Parameters for Microarray Data, Bioinformatics, 19, 1360-1367.

http://www.idav.ucdavis.edu/~dmrocke/

See Also

jggrad2, tranest2

Examples

#library
library(Biobase)
library(LMGene)

#data
data(sample.eS)

tranpar <- tranest2(sample.eS, lambda= 500, alpha=50)
tranpar


[Package LMGene version 1.6.0 Index]