[BioC] Images from exon arrays

Henrik Bengtsson hb at stat.berkeley.edu
Tue Sep 28 03:52:35 CEST 2010

On Fri, Sep 24, 2010 at 10:14 AM, Popovic, Jelena
<jelena.popovic at uky.edu> wrote:
> Thank you, I was also wondering how you generate residual images from exon arrays using affyPLM?

Yes it is possible, and you can see some examples at


and dynamic HTML demos (requires Firefox 3.0+) at


Since this is a question specific to aroma.affymetrix, please repost
to the aroma.* mailing list, cf.



> From: Popovic, Jelena
> Sent: Thursday, September 16, 2010 3:42 PM
> To: 'bioconductor at stat.math.ethz.ch'
> Subject: Images from exon arrays
> Hi,
> I have been using R (R x64 2.11.1)  for generating images from CEL files, using the standard affymetrix gene array. I was wondering if this is possible using the exon array? I tried to do it with the standard packages, but it did not work. Here are the steps that I would normally do using gene array:
> 1.Change directory
> 2.Load Affy and AffyPLM package
> 3. object<-ReadAffy()
> 4. newobject<-fitPLM(object)
> 5.image(newobject,which=1,"resids")
> Is it possible to generate images for exon arrays and if so how do I do it?
> Thank you
>        [[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list