normalize.loess: Scale microarray data

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

Scale microarray data

Description

Normalizes arrays using loess.

Usage

normalize.loess(mat, subset = sample(1:(dim(mat)[1]), min(c(5000,
                 nrow(mat)))), epsilon = 10^-2, maxit = 1, log.it =
                 TRUE, verbose = TRUE, span = 2/3, family.loess =
                 "symmetric")
normalize.AffyBatch.loess(abatch,type=c("together","pmonly","mmonly","separate"), ...)

Arguments

mat	a matrix with columns containing the values of the chips to normalize.
abatch	an AffyBatch object.
subset	a subset of the data to fit a loess to.
epsilon	a tolerance value (supposed to be a small value - used as a stopping criterion).
maxit	maximum number of iterations.
log.it	logical. If TRUE it takes the log2 of mat
verbose	logical. If TRUE displays current pair of chip being worked on.
span	parameter to be passed the function loess
family.loess	parameter to be passed the function loess. "gaussian" or "symmetric" are acceptable values for this parameter.
type	A string specifying how the normalization should be applied. See details for more.
...	any of the options of normalize.loess you would like to modify (described above).

Details

The type argument should be one of "separate","pmonly","mmonly","together" which indicates whether to normalize only one probe type (PM,MM) or both together or separately.

See Also

normalize

Examples

if (require(affydata)) {
  #data(Dilution)
  #x <- pm(Dilution[,1:3])
  #mva.pairs(x)
  #x <- normalize.loess(x,subset=1:nrow(x))
  #mva.pairs(x)
}

Bioconductor/affy documentation built on July 21, 2023, 5:23 p.m.