[BioC] Using a custom CDF file

[Nathan Haigh]

James W. MacDonald wrote:
> Hi Nathan,
>
> Nathan Haigh wrote:
>> I'm using the xspecies [1] approach of hybridising gDNA to the Affy ATH1
>> chip. Using these, one masks out low intensity probes and creates a new
>> CDF file - this is done several times using a different intensity
>> threshold. I then want to analyse RNA hybs to the ATH1 chip using each
>> of these different CDF files.
>>
>> Is it possible, for example, to tell ReadAffy() to use a certain CDF
>> file? If so, I could write a nice R script to do all the processing etc.
>> Or do I have to make a CDF package? If so, how/when do I specify the CDF
>> file to use?
>
> ReadAffy() doesn't use a cdf file. Rather, it uses either a cdf
> package or a cdf environment, both of which are created using the
> makecdfenv package. It would be simple to either make a series of cdf
> packages or cdfenvs and then use ReadAffy() using the 'cdfname'
> argument to point to each of the different packages in turn.
>
> There are tradeoffs to using either approach. If you build the
> packages, you have to install which requires extra work on both
> Windows and MacOS. However, the packages are more persistent than the
> envs which only exist for the current working session unless you
> save() them somewhere and load() them prior to running an analysis.
>
> Best,
>
> Jim
>

Thanks for the clear help - I think the envs will be most suitable for
my purpose - I'll give it a go soon.

Cheers
Nathan