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affy

justrma

Read CEL files into an ExpressionSet

Description

Read CEL files and compute an expression measure without using an AffyBatch.

Usage

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)

Arguments

`...`	file names separated by comma.
`filenames`	file names in a character vector.
`phenoData`	an `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`, then overrides what is in `rm.mask` and `rm.oultiers`.
`hdf5`	use of hdf5 ? (not available yet)
`hdf5FilePath`	a filename to use with hdf5 (not available yet).
`verbose`	verbosity flag.
`widget`	a logical specifying if widgets should be used.
`celfile.path`	a character denoting the path `ReadAffy` should look for cel files.
`sampleNames`	a character vector of sample names to be used in the `AffyBatch`.
`normalize`	logical value. If `TRUE`, then normalize data using quantile normalization.
`background`	logical value. If `TRUE`, then background correct using RMA background correction.
`bgversion`	integer value indicating which RMA background to use 1: use background similar to pure R rma background given in affy version 1.0 - 1.0.2 2: use background similar to pure R rma background given in affy version 1.1 and above
`destructive`	logical value. If `TRUE`, then works on the PM matrix in place as much as possible, good for large datasets.
`cdfname`	Used to specify the name of an alternative cdf package. If set to `NULL`, then the usual cdf package based on Affymetrix' mappings will be used.

Details

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.

Value

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

Author(s)

In the beginning: James MacDonald <jmacdon@med.umich.edu> Supporting routines, maintenance and just.rma: Ben Bolstad <bmb@bmbolstad.com>