[BioC] HGU95a and HGU95av2 with gcrma

Wolfgang Huber huber at ebi.ac.uk
Tue Nov 23 13:54:53 CET 2004

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$dat)
[1] "hgu95av12mix"
> hgu95av12mixcdf <- rawc$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?


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