[BioC] reducing gene number in affybatch objects

Hinnerk Boriss boriss at izbi.uni-leipzig.de
Fri May 23 00:06:57 MEST 2003


> 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)
> 

Rafael, I seem to be missing something. I've done the following:

library(hgu95acdf) #probably already loaded
takeout <- ls(hgu95acdf)[1001:12626]
rm(list=takeout,envir=hgu95acdf)
> junkab <- ReadAffy(widget=T) # reading in 4 hgu95av2 chips
> junkab
AffyBatch object
size of arrays=640x640 features (12804 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=4
number of genes=12625
annotation=hgu95av2
notes= 

Hmm, this still gives me all genes, even though the cdfenv has now only
1000 genes. Am I doing something wrong here?

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

I know, and I do appreciate those other aspects!

> > > Yours dreaming of good old plob objects,
> > 
> > The release 1.0 of the package is still available for 
> download I think...

Laurent, will the release 1.0 be compatible with Wolfgang Huber's vsn
package? I am afraid not. 

Best,
Hinnerk



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