[BioC] reducing gene number in affybatch objects

[Rafael A. Irizarry]

as pointed out by laurent, this not something you want to do for serious
analysis. hinnek asked for something to make
examples in class go a little faster, for which i think this approach is
totally ok.

On Fri, 23 May 2003, Laurent Gautier wrote:

> On Thu, May 22, 2003 at 05:07:46PM -0400, Rafael A. Irizarry wrote:
> > 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.
> 
> I would like to stress that hgu95av2cdf *WAS* included in the package.
> It is now in a external package of example data (package 'affydata').
> 
> I would also like to comment on the approach you suggest. It is a nice
> idea, but can shoot in one's foot. The normalization methods work
> on "probes" (the slot 'exprs' in the AffyBatch). Some of these methods
> work with PMs, some with all the probes without considering the mapping
> (PM, MM or else). By modifying the associated cdfenv, one only modifies
> the mapping. Comparison of the processing methods of the data could be
> risky (and I would suspect that a teaching session would make students
> have a glance at that). The use of a subset of affyids suggested before
> is safe.
> 
> Finally, to answer the qustion about VSN and affy 1.0. It won't work out
> of the box, but the mecanism for additional processing methods was already
> there. You could port vsn for Plobs.
> 
> 
> 
> Hopin'  it helps,
> 
> 
> 
> L.
> 
> 
> 
>  
> > 
> > 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
> > > 
> > > 
> > 
> 
> -- 
> --------------------------------------------------------------
> 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
>