readCel2eSet: Read celfiles into an ExpressionSet object.
In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description Usage Arguments Details Value Author(s) Examples

This is a wrapper for ReadAffy that returns an ExpressionSet object rather than an AffyBatch. This is particularly usefiles for arrays for which we have or need no CDF environment.

1	readCel2eSet(filename, adf, path=".", rotated=FALSE, ...)

`filename`	Character vector with CEL file names. Either `filename` or `adf` need to be specified, but not both.
`adf`	Object of class `AnnotatedDataFrame`.
`path`	Character scalar with path to CEL files.
`rotated`	Logical scalar, see details.
`...`	Further arguments that are passed on to `new("ExpressionSet")`.

The rotate options allows to deal with different versions of the scanner software. Older versions rotated the image by 90 degrees, newer ones do not. Use the default rotated=FALSE for CEL files produced by the newer version.

ExpressionSet object.

W. Huber

## To test the rotation, look at the scatterplot between two DNA hybes
## that were measured with scanner software that rotated (041120) and did
## not rotate (060125)
##
## cp /ebi/research/huber/Projects/tilingArray/Celfiles/041120_S96genDNA_re-hybe.cel.gz ~/p/tmp
## cp /ebi/research/huber/Projects/allelicTranscription/celfiles_allelictrans/060125_S96_genomicDNA.zip ~/p/tmp
## cd ~/p/tmp
## gunzip 041120_S96genDNA_re-hybe.cel.gz
## unzip 060125_S96_genomicDNA.zip
##
## Not run: 
library("affy")
options(error=recover)

e1 = readCel2eSet("041120_S96genDNA_re-hybe.cel", rotated=TRUE)
e2 = readCel2eSet("060125_S96_genomicDNA.CEL")

smoothScatter(log(exprs(e1)), log(exprs(e2)), nrpoints=0)

## End(Not run)