[BioC] Custom CDF Files - howto ?

[Rhonda DeCook]

Rich,

Can you tell us a little more.  How was your custom CDF file created?  It seems 
like R is not recognizing the file in your directory as a CDF file.  I created 
a custom CDF file recently for the ATH1 chip that removed known 'SFP' probe 
pairs using the 'altcdfenv' package and a modification of functions in 
the 'matchprobes' package (provided to me by Holger Schwender after I posted  
to this list).  I eventually got everything running with the new CDF file 
assigned to my affybatch and I didn't have to go into the CEL files and hand 
edit the CDF file name on any of the 30 chips.  I'll see if I can help after 
you send a little more info.

Rhonda



> 
> I have created a custom CDF file.
> 
> The purpose is to measure the expression of splice
> variations.
> 
> I place the file in the same directory as the CEL
> files and crank up R and do the usual BIOC
> incantation.
> 
> Based on a suggestion offered by the brainiacs at
> University of Michigan (
> 
http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm
#How_to_use_the_custom_CDF_file:_
> )
> I try something like this ...
> 
> data<-ReadAffy();
> data at cdfName<-"NEW.CDF"
> 
> But subsequent data processing calls attempt to
> connect to the internet and get a CDF file from there.
> 
> Obviously, I missing something.
> 
> Anybody got any ideas?
> 
> Please add to any "RTFM" responses a specific FM to
> read.
> 
> Thanks!
> 
> Rich
> 
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