[BioC] split.AffyBatch

[Laurent Gautier]

As I was pointed out by Ben Bolstad, split.AffyBatch _does_ behave 
erratically.

After a quick look changes were made elsewhere in the subsetting 
functions for objects of class AffyBatch, and apparently these changes 
had a sneaky incidence on the outcome of (at least) split.AffyBatch.

The inheritance of S4-style methods works better than in the old days 
this function was written, and a quick and dirty temporary fix for the 
problem is may be to do:

rm("split.AffyBatch", envir=as.environment("package:affy"))
##(quite a fix, ha... just remove the whole...)

Ex:
library(affy)
rm("split.AffyBatch", envir=as.environment("package:affy"))
library(affydata)
data(Dilution)
sp <- split(Dilution, pData(Dilution)$liver)
print(sp)

However, now when using the function there are warning messages.
I would propose to rehabilitate the functions recently declared as 
"deprecated" (since these changes break some methods inherited from 
exprSet(*))... but I suspect that the changes to the subsetting of 
objects of class AffyBatch were asked by users.

Anyone to oppose/confirm/debate ?


L.

(*): an other option is to override the method with methods (and with 
code redundancy)...