[BioC] Custom CDF files

[Ken Simpson]

Rich,

Unless I am mistaken, it doesn't sound like you have made a CDF
environment for your custom probe sets yet.  You will have to do that
first.  You need to use makecdfenv to create a package containing the
environment, then install the package.  Supposing your CDF package is
called  newcdf, you could then do

Data <- ReadAffy()
Data at cdfName <- "new"       # I think you have to omit the "cdf" part

As for using gcrma, you'll have to make a separate probe package for this.
 IIRC Wolfgang Huber posted a way to do that fairly recently, using
matchprobes - try the mailing list archive.

Cheers,

Ken

>    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
>