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

[James W. MacDonald]

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?

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.

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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