just.rma(..., 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, background=TRUE, normalize=TRUE, bgversion=2, destructive=FALSE, cdfname = NULL)
justRMA(..., filenames=character(0), widget=getOption("BioC")$affy$use.widgets, compress=getOption("BioC")$affy$compress.cel, celfile.path=getwd(), sampleNames=NULL, phenoData=NULL, description=NULL, notes="", rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, hdf5=FALSE, hdf5FilePath=NULL,verbose=FALSE, normalize=TRUE, background=TRUE, bgversion=2, destructive=FALSE, cdfname = NULL)AnnotatedDataFrame
object.MIAME object.NA?NA?TRUE, then overrides what is in
rm.mask and rm.oultiers.ReadAffy should look
for cel files.AffyBatch.TRUE, then normalize data using
quantile normalization.TRUE, then background correct
using RMA background correction.TRUE, then works on the PM matrix
in place as much as possible, good for large datasets.NULL, then the usual cdf package based on Affymetrix' mappings
will be used.ExpressionSet object, containing expression values identical to
what one would get from running rma on an AffyBatch.
justRMA is a wrapper for just.rma that permits the user to read
in phenoData, MIAME information, and CEL files using widgets. One can also
define files where to read phenoData and MIAME information.If the function is called with no arguments justRMA(), then all the CEL
files in the working directory are read, converted to an expression measure
using RMA and put into an
ExpressionSet.
However, the arguments give the user great flexibility.
phenoData is read using read.AnnotatedDataFrame.
If a character is given, it tries to read the file with that name to obtain the
AnnotatedDataFrame object as described in read.AnnotatedDataFrame.
If left NULL and widget=FALSE (widget=TRUE is not currently
supported), then a default object is created.
It will be an object of class AnnotatedDataFrame
with its pData being a data.frame with column x indexing the CEL files.
description is read using read.MIAME. If a
character is given, it tries to read the file with that name to obtain a
MIAME instance. If left NULL but widget=TRUE, then
widgets are used. If left NULL and widget=FALSE, then an
empty instance of MIAME is created.
The arguments rm.masks, rm.outliers, rm.extra are
passed along to the function read.celfile.
rma, read.affybatch