read.probematrix: Read CEL file data into PM or MM matrices

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

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 [e-mail]

See Also

AffyBatch, read.affybatch

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