[BioC] Custom CDF Files - howto ?

[Richard Finney]

Rhonda,
   I wrote a program that takes an original text CDF
file as a template and writes out my revised "units"
(Affyspeak for probesets).  The revised units are sets
of probes that map to a quality filtered set of
transcripts: higher quality transcripts, chimerics
stripped, latest Genbank records, etc.  A unit
(probeset) can get very large and I'm going to try and
 reuse probes if it's possible  (sometimes probes
match to mulitple genes).

I'm hoping that this will work with RMA but I am
concerned about GCRMA since it relies on additional
probeset sequence information which is originally
available in the "probetab" files provided by
Affymetrix.

Another possible concern is if Robert Genetlemen is
right and I have to change the chipname in the CEL
file.  This is, of course, a piece of cake with TEXT
CEL files.  Binary CEL files will require a little
more delicate approach: writing a quick hack program
to replace the old string.

I will certainly check out the altcdfenv package.

Again, if anyone has any caveats when dealing with
this, pleas let me and everybody else know about it.

Rich


--- Rhonda DeCook <rdecook at iastate.edu> wrote:

> 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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> 
> 
> 
> 
> 
>