tilingArray (version 1.50.0)

readCel2eSet: Read celfiles into an ExpressionSet object.

Description

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.

Usage

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

Arguments

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").

Value

ExpressionSet object.

Details

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.

Examples

## 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)