[BioC] CDF/Probe/Annotation for GNF1m custom chip

[Cei Abreu-Goodger]

Thanks for the reply Kasper.

I now have cdf and probe packages for Mouse and Human GNF affy chips. Is
there some way I could contribute these to bioconductor?

Cei

On Fri, 6 Apr 2007, Kasper Daniel Hansen wrote:

>
> On Apr 6, 2007, at 2:02 PM, Cei Abreu-Goodger wrote:
>
> >
> > Hello all,
> >
> > I am trying to use affylmGUI to pre-process data from a GNF1m
> > custom Affy
> > chip. I'm on MacOSX 10.4.9, R 2.4.1, Bioconductor 1.9.
> >
> > I downloaded the series CEL file from GEO, and I used
> > make.cdf.package to produce a CDF environment for this chip. I get a
> > warning, but I can install the package anyway, so maybe it's working?
> > Warning message:
> > incomplete final line found by readLines on
> > '/Library/Frameworks/R.framework/Versions/2.4/Resources/library/
> > makecdfenv/Code/DESCRIPTION'
> >
> > But when I try to normalize my CEL files, I get an error stating
> > that the
> > variable "gngnf1musaprobe" was not found. I imagine that, just as I
> > created a custom CDF environment, I now need custom probe and maybe
> > annotation objects. Yet I couldn't find something to indicate how to
> > create these.
> > The affylmGUI help says to ask this mailing list. Does anyone have any
> > suggestions?
>
> I guess you want to use gcrma. Yes, in that case you need a probe
> package, which you can create using the matchprobes package.
> Essentially you will need a file describing the sequence of the
> probes spotted on the array. The probe package is (essentially, there
> is some other optional information) a table like
>    x y sequence
>   1 1 AGCT...
> This information is certainly not always available, especially since
> it is not your chip. Sometimes you need a FASTA file, sometimes you
> can find it in the CDF file or somewhere else.
>
> You only need a probe package if you are using a preprocessing
> procedure that takes the sequence composition of the probes into
> account - like gcrma.
>
> You will not need an annotation package before you want to start to
> make sense of what "genes" are DE. And you might not need an
> annotation package for that, depending on what kind of interpretation
> you want to do. You might need to do some GO annotation in order to
> do a GO enrichment analysis.
>
> Kasper
>
> > Thanks,
> >
> > Cei
> >
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>