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BufferedMatrix (version 1.36.0)

BufferedMatrix.justRMA: Use BufferedMatrix objects to facilitate RMA computation with low memory overhead

Description

Read CEL data into BufferedMatrix objects.

Usage

BufferedMatrix.justRMA(..., filenames=character(0),celfile.path=NULL,
                     phenoData=new("AnnotatedDataFrame"),
                     description=NULL,
                     notes="",
                     verbose=FALSE, background=TRUE, normalize=TRUE,
                     cdfname = NULL)

Arguments

...
file names separated by comma.
filenames
file names in a character vector.
celfile.path
path where CEL files are located
phenoData
a AnnotatedDataFrame object
description
a MIAME object
notes
notes
verbose
verbosity flag
normalize
logical value. If TRUE normalize data using quantile normalization
background
logical value. If TRUE background correct using RMA background correction
cdfname
Used to specify the name of an alternative cdf package. If set to NULL, the usual cdf package based on Affymetrix' mappings will be used.

Value

  • An ExpressionSet object, containing expression values identical to what one would get from running rma on an AffyBatch.

See Also

BufferedMatrix, BufferedMatrix.read.probematrix