[BioC] HGU95a and HGU95av2 with gcrma

[Zhijin Wu]

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 
affinity.info1=compute.affinities("hgu95a")  
affinity.info2=compute.affinities("hgu95av2")
affinity.mix12=combineAffyBatch(list(affinity.info1,affinity.info2),
  c("hgu95aprobe","hgu95av2probe"), "hgu95av12mix")

Then save affinity.mix12 for future use. When calling gcrma, use
"affinity.info=affinity.mix12"


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
>      Wolfgang
> 
> -------- 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)
> [1] "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?
> 
> Vincent
> 
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