R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Sparse PCs of Microarrays

arrayspc

R Documentation

Sparse PCs of Microarrays

Description

Sparse PC by iterative SVD and soft-thresholding

Usage

arrayspc(x,K=1,para,use.corr=FALSE, max.iter=100,trace=FALSE,eps=1e-3)

Arguments

`x`	The microarray matrix.
`K`	Number of components. Default is 1.
`para`	The thresholding parameters. A vector of length K.
`use.corr`	Perform PCA on the correlation matrix? This option is only effective when the argument type is set "data".
`max.iter`	Maximum number of iterations.
`trace`	If TRUE, prints out its progress.
`eps`	Convergence criterion.

Details

The function is equivalent to a special case of spca() with the quadratic penalty=infinity. It is specifically designed for the case p>>n, like microarrays.

Value

A "arrayspc" object is returned.

Author(s)

Hui Zou, Trevor Hastie and Robert Tibshirani

References

Zou, H., Hastie, T. and Tibshirani, R. (2004) "Sparse principal component analysis" Technical report, Statistics Dept. Stanford University