[BioC] Using a custom CDF file

[James W. MacDonald]

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


> 
> I'm new to R/Bioconductor, so would appreciate any help towards this.
> 
> Cheers
> Nathan
> 
> [1] http://affymetrix.arabidopsis.info/xspecies/
> 
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