Images from exon arrays
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@popovic-jelena-4266
Last seen 10.2 years ago
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]]
affy affyPLM affy affyPLM • 1.2k views
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@henrik-bengtsson-4333
Last seen 6 months ago
United States
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 >
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@popovic-jelena-4266
Last seen 10.2 years ago
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]]
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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 >
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