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affy (version 1.50.0)

read.probematrix: 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.

See Also

AffyBatch, read.affybatch