justRMA {affy}R Documentation

Read CEL files into an AffyBatch

Description

Read CEL files and compute an expression measure using affybatch.

Usage

just.rma(..., filenames = character(0),
               phenoData = new("phenoData"),
               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)

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)

Arguments

... file names separated by comma.
filenames file names in a character vector.
phenoData a phenoData 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
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 normalize data using quantile normalization
background logical value. If TRUE 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 works on the PM matrix in place as much as possible, good for large datasets.

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 call 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 exprSet. However, the arguments give the user great flexibility.

phenoData is read using read.phenoData. If a character is given it tries to read the file with that name to obtain the phenoData object as described in read.phenoData. If left NULL but widget=TRUE then widgets are used. If left NULL and widget=FALSE then a default object is created. It will be an object of class phenoData with new("phenoData",pData=data.frame(x=1:length(CELfiles)),varLabels=list(x="arbitrary number"))

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 exprSet object.

Author(s)

In the beginning: James MacDonald <jmacdon@med.umich.edu> Supporting routines, maintainence and just.rma: Ben Bolstad <bolstad@stat.berkeley.edu>

See Also

rma,ReadAffy

Examples



[Package affy version 1.8.1 Index]