[BioC] Affy normalization with custom chip.

[Cei Abreu-Goodger]

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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