affy: read.probematrix – R documentation

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Documentation

affy

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.

Author(s)

Ben Bolstad bmb@bmbolstad.com