| readCel2eSet {tilingArray} | R Documentation |
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.
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")
library("geneplotter")
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)