[BioC] affyPara

Valerie Obenchain vobencha at fhcrc.org
Sat Oct 16 01:12:27 CEST 2010

Hi Daniela,

On 10/14/2010 04:17 PM, danieladna wrote:
> Hi Valerie,
> Unfortunately ReadAffy doesn't manage to load one file only.
ReadAffy can read a single file at a time. See the examples in ?ReadAffy
then try

    celpath <- system.file("celfiles", package="affydata")
    fns <- list.celfiles(path=celpath,full.names=TRUE)
    # read a single file
    abatch <- ReadAffy(filenames=fns[2])
    # alternatively, read all files in a directory
    abatch <- ReadAffy(celfile.path=celpath)

> I do manage to load all CEL files that are in the current location though.
> Therefore I use:
> data<-ReadAffy()
> data at cdfName<-"cdfname"
> eset<-rma(data)
It is ok if you want to use all files or a single file for this example;
a single file would simply be faster. I am interested in the output of
the example because I want to confirm that no CDF errors are thrown when
reading a cel file with the same huex10stv2hsensecdf package you are
using in your affyPara code. I'd like to help further with this problem
but need a couple of things from you in order to do so.  Please

(1) run this code and provide the output

    data <- ReadAffy()
    data at cdfName <- "huex10stv2hsensecdf"
    est <- rma(data)

(2) send me the huex10stv2hsensecdf package you are using

Thank you,

> I get most of my CDF files from Brainarray.
> Thanks for your help,
> Daniela
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