read.probematrix {affy}R Documentation

Read CEL file data into PM or MM matrices

Description

Read CEL data into matrices.

Usage

read.probematrix(..., filenames = character(0),
               phenoData = new("phenoData"),
               description = NULL,
               notes = "",
               compress = getOption("BioC")$affy$compress.cel,
               rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
               verbose = FALSE,which="pm")

Arguments

... file names separated by comma.
filenames file names in a character vector.
phenoData a phenoData object
description a MIAME object
notes notes
compress are the CEL files compressed ?
rm.mask should the spots marked as 'MASKS' set to NA ?
rm.outliers should the spots marked as 'OUTLIERS' set to NA
rm.extra if TRUE, overrides what is in rm.mask and rm.oultiers
verbose verbosity flag
which should be either "pm", "mm" or "both"

Details

Value

A list of one or two matrices. Each matrix is either PM or MM data. No AffyBatch is created.

Author(s)

Ben Bolstad bolstad@stat.berkeley.edu

See Also

AffyBatch, read.affybatch

Examples



[Package affy version 1.8.1 Index]