[BioC] HGU95a and HGU95av2 with gcrma
zwu at jhsph.edu
Tue Nov 23 19:36:50 CET 2004
SInce the cdf environment generated in combineAffyBatch is not a package
for a real array, there is no "xy2i" function associated with it, which
compute.affinities() uses to link probe sequence and probe location.
One options it to compute
Then save affinity.mix12 for future use. When calling gcrma, use
On Tue, 23 Nov 2004, Wolfgang Huber wrote:
> Question to the gcrma people - how can one make it use a CDF environment
> that is sitting in the ".GlobalEnv"? (or how to manipulte an environment
> so that it is recognized?)
> Best regards
> -------- Original Message --------
> Subject: Re: [BioC] HGU95a and HGU95av2 with gcrma
> Date: Tue, 23 Nov 2004 11:47:41 +0100 (CET)
> From: Vincent Detours <vdetours at ulb.ac.be>
> To: Wolfgang Huber <huber at ebi.ac.uk>
> > create a variable with that name in your top level workspace that is the
> > CDF environment, e.g.
> > hgu95av12mixcdf = rawc$cdf
> > Let me know if that helps.
> Wolfgang, I tryed it
> > cdfName(rawc$dat)
>  "hgu95av12mix"
> > hgu95av12mixcdf <- rawc$cdf
> > es <- gcrma(rawc$dat)
> Computing affinities.Error in compute.affinities(cdfName(object),
> verbose = verbose) :
> NAs are not allowed in subscripted assignments
> It doesn't work with gcrma (but it does work with rma). Making a
> package from rawc$cdf, or forcing getCDF() to use the variable
> hgu95av12mixcdf would probably work. Any idea of how to do this?
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