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

[Kasper Daniel Hansen]

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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