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("AnnotatedDataFrame"),
                 description = NULL,
                 notes = "",
                 compress = getOption("BioC")$affy$compress.cel,
                 rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
                 verbose = FALSE, which = "pm", cdfname = NULL)

Arguments

... file names separated by comma.
filenames file names in a character vector.
phenoData a AnnotatedDataFrame 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".
cdfname Used to specify the name of an alternative cdf package. If set to NULL, the usual cdf package based on Affymetrix's mappings will be used.

Value

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

Author(s)

Ben Bolstad bmb@bmbolstad.com

See Also

AffyBatch, read.affybatch


[Package affy version 1.24.2 Index]