[BioC] combineAffyBatch problem

James W. MacDonald jmacdon at med.umich.edu
Mon Aug 7 17:29:19 CEST 2006

Hi Catherine,

Catherine Dumur wrote:
> Dear Wolfgang and Bioconductor people,
> I am using the combineAffyBatch function from the matchprobes package 
> regularly now, and I am very pleased with its performance.
> However, I was wondering if you can help me with the following:
> I understand that every time I run the function, a new .CDF object is 
> created and this takes a considerable amount of time. I was wondering if 
> we can re-use an existing "newcdf" object when performing new analysis 
> where the same two types of arrays are used. In other words, since I am 
> always combining the same 2 types Affy chips, the newcdf object should 
> be the same. If I use that object from previous sessions, I shouldn't be 
> creating a new one every time.

You are correct, you _shouldn't_ be creating a new one every time. 
Instead, you should save() the newcdf object and load() it back in when 
you need it. An example would be:

save(newcdf, file="newcdf.Rda")

If you use this newcdf regularly, you might even want to build a data 
package. See 'Writing R Extensions' for more information.



> I would greatly appreciate it if you could tell me if that is feasible, 
> and if it is, how can I  do it.
> Thank you very much for your attention to this issue.
> Cathy

James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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