read.celfiles: Parser to CEL files
In oligo: Preprocessing tools for oligonucleotide arrays

Description Usage Arguments Details Value See Also Examples

Reads CEL files.

read.celfiles(..., filenames, pkgname, phenoData, featureData,
experimentData, protocolData, notes, verbose=TRUE, sampleNames,
rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, checkType=TRUE)

read.celfiles2(channel1, channel2, pkgname, phenoData, featureData,
experimentData, protocolData, notes, verbose=TRUE, sampleNames,
rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, checkType=TRUE)

`...`	names of files to be read.
`filenames`	a `character` vector with the CEL filenames.
`channel1`	a `character` vector with the CEL filenames for the first 'channel' on a Tiling application
`channel2`	a `character` vector with the CEL filenames for the second 'channel' on a Tiling application
`pkgname`	alternative data package to be loaded.
`phenoData`	`phenoData`
`featureData`	`featureData`
`experimentData`	`experimentData`
`protocolData`	`protocolData`
`notes`	`notes`
`verbose`	`logical`
`sampleNames`	`character` vector with sample names (usually better descriptors than the filenames)
`rm.mask`	`logical`. Read masked?
`rm.outliers`	`logical`. Remove outliers?
`rm.extra`	`logical`. Remove extra?
`checkType`	`logical`. Check type of each file? This can be time consuming.

When using 'affyio' to read in CEL files, the user can read compressed CEL files (CEL.gz). Additionally, 'affyio' is much faster than 'affxparser'.

The function guesses which annotation package to use from the header of the CEL file. The user can also provide the name of the annotaion package to be used (via the pkgname argument). If the annotation package cannot be loaded, the function returns an error. If the annotation package is not available from BioConductor, one can use the pdInfoBuilder package to build one.

`ExpressionFeatureSet`	if Expresssion arrays
`ExonFeatureSet`	if Exon arrays
`SnpFeatureSet`	if SNP arrays
`TilingFeatureSet`	if Tiling arrays

list.celfiles, read.xysfiles

if(require(pd.mapping50k.xba240) & require(hapmap100kxba)){
celPath <- system.file("celFiles", package="hapmap100kxba")
celFiles <- list.celfiles(celPath, full.name=TRUE)
affySnpFeatureSet <- read.celfiles(celFiles)
}

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':

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

Loading required package: oligoClasses
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
Welcome to oligoClasses version 1.38.0
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: Biostrings
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Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

================================================================================
Welcome to oligo version 1.40.2
================================================================================
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Loading required package: pd.mapping50k.xba240
Loading required package: RSQLite
Loading required package: DBI
Loading required package: hapmap100kxba
Warning messages:
1: Couldn't set synchronous mode: database is locked
Use `synchronous` = NULL to turn off this warning. 
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'hapmap100kxba'