read.affybatch: Read CEL files into an AffyBatch

Description

Read CEL files into an Affybatch.

Usage

read.affybatch(..., 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,sd=FALSE, cdfname = NULL)
ReadAffy(..., filenames=character(0), widget=getOption("BioC")$affy$use.widgets, compress=getOption("BioC")$affy$compress.cel, celfile.path=NULL, sampleNames=NULL, phenoData=NULL, description=NULL, notes="", rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE,sd=FALSE, cdfname = NULL)

Arguments

...

file names separated by comma.

filenames

file names in a character vector.

phenoData

an AnnotatedDataFrame object, a character of length one, or a data.frame.

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.

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.

should the standard deviation values in the CEL file be read in? Since these are typically not used default is not to read them in. This also save lots of memory.

cdfname

used to specify the name of an alternative cdf package. If set to NULL, then the usual cdf package based on Affymetrix's mappings will be used.

Value

An AffyBatch object.

Details

ReadAffy is a wrapper for read.affybatch 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 ReadAffy() all the CEL files in the working directory are read and put into an AffyBatch. However, the arguments give the user great flexibility. If phenoData is a character vector of length 1, the function read.AnnotatedDataFrame is called to read a file of that name and produce the AnnotationDataFrame object with the sample metadata. If phenoData is a data.frame, it is converted to an AnnotatedDataFrame. If it is NULL and widget=FALSE (widget=TRUE is not currently supported), then a default object of class AnnotatedDataFrame is created, whose pData is a data.frame with rownames being the names of the CEL files, and with one column sample with an integer index.

AllButCelsForReadAffy is an internal function that gets called by ReadAffy. It gets all the information except the cel intensities.

description is read using read.MIAME. If a character is given, then 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.

Examples

Run this code

if(require(affydata)){
     celpath <- system.file("celfiles", package="affydata")
     fns <- list.celfiles(path=celpath,full.names=TRUE)
 
     cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
     ##read a binary celfile
     abatch <- ReadAffy(filenames=fns[1])
     ##read a text celfile
     abatch <- ReadAffy(filenames=fns[2])
     ##read all files in that dir
     abatch <- ReadAffy(celfile.path=celpath)
}