[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

  http://www.aroma-project.org/screenshots/

and dynamic HTML demos (requires Firefox 3.0+) at

  http://www.aroma-project.org/demos/

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

  http://www.aroma-project.org/forum/

/Henrik

>
>
> 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]]
>
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