normalize.loess: Scale microarray data

In affy: Methods for Affymetrix Oligonucleotide Arrays

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)
}

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Loading required package: affydata
     Package    LibPath                         Item      
[1,] "affydata" "/usr/local/lib/R/site-library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
NULL

affy documentation built on Nov. 8, 2020, 8:18 p.m.