read.affybatch: Read CEL files into an AffyBatch
In affy: Methods for Affymetrix Oligonucleotide Arrays

Description Usage Arguments Details Value Author(s) See Also Examples

Read CEL files into an Affybatch.

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)

`...`	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`.
`sd`	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.

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.

An AffyBatch object.

Ben Bolstad bmb@bmbolstad.com (read.affybatch), Laurent Gautier, and Rafael A. Irizarry (ReadAffy)

AffyBatch

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)
}

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: affydata
     Package    LibPath                   Item      
[1,] "affydata" "/usr/lib/R/site-library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
Reading files:
 /usr/lib/R/site-library/affydata/celfiles/binary.cel
/usr/lib/R/site-library/affydata/celfiles/text.cel