[BioC] How do I install custom made CDF in Bioconductor

[Ruppert Valentino]

>Ruppert,
>
>I think you need to give more information before anybody can help. When
>you say custom CDF, does this mean you are using the altcdfenv package,
>or are you somehow modifying the CDF by hand?

Hello Jim,
             Thank you for the reply. Basically I am trying to create a new 
CDF which has mixture probes from U95ver2a and U133ver2.0. On the Affy site 
they don't have this so I have to create it myself. I am not sure what is 
the best way to do this and on what platform. I tried to find a primer or 
information on how to create custom made CDF but they don't tell you what 
the structure of the CDF file should be. Also the other issue is I am using 
R 2.1.1 on Windows but in the manual they say if you are using Windows then 
you have to do more to creat and upload the CDF environment. Basically I got 
the CDF file in ASCII format and now trying to create a CDF package that I 
can use to analyse chips which are mixture of U133 and U95 (not good idea 
due to a lot of variation but I have to do it).

>In general, you need to run a CDF file through the makecdfenv package
>(using either make.cdf.env() or make.cdf.package()) before it can be
>used. Then if you want to use that cdvenv with your celfiles, you would
>have to read the celfiles into an AffyBatch and then change the cdfName
>slot of the AffyBatch to point to your modified cdfenv.
>
>dat <- ReadAffy()
>dat at cdfName <- "nameofyourcdfenv"
>
>Then proceed as usual.

I will do this thank you. Will this work on R 2.1.1 on Windows or do i need 
to do it on Linux?

Also what is the minimum requirement for the structure of the CDF file?

Thank you

Ruppert.

>HTH,
>
>Jim
>
>
>
>Ruppert Valentino wrote:
>
> >Hello,
> >         I have created a custom made CDF file and am trying to install
>that
> >to analyse Affymetrix chip files. Can anyone tell me what format should 
>the
> >CDF files be in? and when does the CEL file has a CDF file attached to 
>it,
> >if so how can I update the CEL file data with my custom made CDF?
> >
> >Many thanks
> >
> >Raphael.
> >
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> >
>