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]]
The aroma.affymetrix package can generate images (also PNGs) for all
Affymetrix chip types, cf. http://www.aroma-project.org/
/Henrik
On Thu, Sep 16, 2010 at 12:41 PM, Popovic, Jelena
<jelena.popovic at="" uky.edu=""> wrote:
> 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
>
Thank you, I was also wondering how you generate residual images from
exon arrays using affyPLM?
From: Popovic, Jelena
Sent: Thursday, September 16, 2010 3:42 PM
To: 'bioconductor@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]]
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]]
>
> _______________________________________________
> 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
>
