[BioC] reducing gene number in affybatch objects

[Rafael A. Irizarry]

you are using hgu95av2. so change it to the following:

1) data(hgu95av2cdf) #probably already loaded... 
2) takeout <- ls(hgu95av2cdf)[1001:12626]
3) rm(list=takeout,envir=hgu95av2cdf)

notice that hgu95av2cdf is included in the affy package (at least up to 
1.1.2) so you dont need to load the library.

Hinnerk Boriss wrote:

> 
> > 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
> 
>