[BioC] Affy normalization with custom chip.

[Jenny Drnevich]

Hi Daniel,

Also, there's a good chance that you won't be able to use gcrma() on 
a custom Affy chip, unless the custom array contains the PM-MM 
pairing, and you have a probe file that contains the amount and 
location of GC content of the probes, in addition to the cdf file. If 
it's a PM only array, you won't be able to do the gc-based background 
correction of gcrma, but you can do the model-based background of rma().

Cheers,
Jenny

At 01:50 PM 6/4/2007, Cei Abreu-Goodger wrote:

>Hi Daniel,
>
>I asked the same a while back. You should start by checking out
>the "makecdfenv" and "matchprobes" vignettes. There should be enough
>information there to get you going. Essentially you have to create your
>own packages for the GNF1M chip and install them.
>
>Cei
>
>
>On Mon, 4 Jun 2007, Daniel Gatti wrote:
>
> > I'm analyzing a publicly available GEO data set (GEO5961) that uses a
> > custom array (GNF1M).  The file download from GEO includes a .CDF file
> > for the array, CEL files and several other files that I'm not 
> familiar with.
> >
> >  > library(gcrma)
> > Loading required package: Biobase
> > Loading required package: tools
> >
> > Welcome to Bioconductor
> >
> >      Vignettes contain introductory material. To view, type
> >      'openVignette()' or start with 'help(Biobase)'. For details
> >      on reading vignettes, see the openVignette help page.
> >
> > Loading required package: affy
> > Loading required package: affyio
> > Loading required package: matchprobes
> > Loading required package: splines
> >  > rawdata = ReadAffy("GSM138562.CEL", "GSM138563.CEL")
> >  > norm = gcrma(rawdata)
> > Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> > encountered:
> > Specified environment does not contain gnGNF1Musa
> > Library - package gngnf1musacdf not installed
> > Data for package affy did not contain gngnf1musacdf
> > Bioconductor - gngnf1musacdf not available
> >
> > How can I load the GPL1073.CDF and GPL1073.probe files for the array
> > into the "environment" so that gcrma() can access them?  I've tried
> > functions like getCDF(), but it's not clear how to specify a local file
> > as the source.  And read.cdffile() reads into an object, but I'm not
> > clear how make that object visible to gcrma().
> >
> > Thanks,
> > Dan Gatti
> > UNC-CH
> >
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>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
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e-mail: drnevich at uiuc.edu