[BioC] adapt exprSet class

[James W. MacDonald]

Hi Sjoerd,

Vosse, S.J. wrote:
> Dear all,
> 
>  
> 
> to add greater structure to the data exported by our package, we have
> been advised to work with S4 classes. As a starting point we would like
> to adapt the exprSet class, by adding new slots for example. I'm having
> a very hard time finding out where to start though. Does anybody have
> any pointers to documentation on S4 classes and the exprSet class?

The exprSet class has been deprecated and will likely be defunct Real 
Soon Now(tm), so you would be advised to use the ExpressionSet class 
instead.

As far as documentation goes, you might look at ?eSet, ?ExpressionSet, 
and the vignettes that come with Biobase, namely

Biobase - An introduction to Biobase and ExpressionSets

and

Biobase - Notes for eSet developers

and

Biobase - quick views of eSet instances

All of which can be accessed most easily by

library(Biobase)
openVignette()

You might also google 's4 15 pages' which will bring up (as the first 
item in the list) a tutorial on the use and care of S4 methods.

Best,

Jim

> 
>  
> 
> Thanking you in advance,
> 
>  
> 
> Sjoerd Vosse
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
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