[BioC] reducing gene number in affybatch objects

[Rafael A. Irizarry]

Hinnek,

i'd like to add there is a simple way to remove genes. its not the best
way but its simple and itll do the trick:
say ab is your affybatch and hgu95acdf is your cdf before your class type:

1) library(hgu95acdf) #probably already loaded
2) takeout <- ls(hgu95acdf)[1001:12626]
3) rm(list=takeout,envir=hgu95acdf)

to get back to original hgu95acdf 
detach("package:hgu95acdf");library(hgu95acdf)

AffyBatch's are not a simple as Plob's, but they make other things 
more efficient. 

On Thu, 22 May 2003, Laurent Gautier wrote:

> On Thu, May 22, 2003 at 03:06:15PM +0200, Hinnerk Boriss wrote:
> > Hi there,
> > 
> > for teaching purposes I would like to cut down the number of genes in
> > affybatch objects so that students won't have to wait that long for
> > their computations. Unfortunately, I cannot figure out how to do that.
> > Any hints? Thanks!
> 
> Cutting down the size of an AffyBatch is not straightforward (for the 
> moment, it should be in the future). There are implications if one
> does so (think about the spatial background correction as done
> in mas 5.0). I believe that the "slowest" part is the computation of
> summary expression values. You may want to investigate the use of the
> parameter 'ids' for the method 'computeExprSet' 
> (or 'summary.subset' for the function 'expresso',
> you can ask for the summary of a given set of affyids).
> 
> 
>  
> > 
> > Yours dreaming of good old plob objects,
> 
> The release 1.0 of the package is still available for download I think...
> ;)
> 
> 
> Hopin' it helps,
> 
> 
> Laurent
> 
> 
> > Hinnerk
> > 
> > _______________________________________________
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> 
> -- 
> --------------------------------------------------------------
> currently at the National Yang-Ming University in Taipei, Taiwan
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent
> 
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