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.
Matrix with maxk
rows and length(x)
columns.
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)