[BioC] Creating Affymetrix CDF files

[Kasper Daniel Hansen]

On Jan 19, 2009, at 12:50 , Srinivas Iyyer wrote:

> Hello:
>
> What is a CDF file and what should be the contents of it (format)  
> and how should I make it.
>
> My question is:
> I have a probe, its coordinates and annotation in tab delim file.
>
>
> Prob X cord <tab> Prob Y cord <tab> type (PM) <tab> pbset name <tab>  
> annotations
>
> I have this for u95av2.
>
> Now I want to run RMA on on u95av2 chip cel files using my probeset  
> definitions. I removed probes that are not part of sequence and many  
> more.
>
> is there a step-wise protocol to make read.celfiles and rma  
> functions understand my definition file.

If you truly want to create a CDF file, you should browse the archives  
- this has been discussed a few times recently. You will need to used  
writeCDF from affxparser.

But it seems like what you want is to modify a CDF environment, and do  
your analysis in Bioconductor. This has also been discussed at length  
- try searching for something like "how do I remove probes from a CDF  
environment".

Kasper