[Bioc-devel] exprSet and friends

Keith Satterley keith at wehi.EDU.AU
Mon Sep 17 02:06:59 CEST 2007

I agree with Wolfgang. Don't make changes so close to a release.

I'm not sure what effect expunging all exprSet methods would have. I currently 
need the exprSet class definition and accessor methods to get expr and se.expr 
data from exprSet objects. Users may have saved there data previously using 
affylmGUI. A user may wish to open that data file again using a current version 
of affylmGUI. affylmGUI supports this by opening the old data file, getting the 
expr and se.expr data from the exprSet object. affylmGUI will then save the data 
in an updated version of the affylmGUI data object, if the user requests it. I 
don't wish to alter this process before the R 2.6.0 release date, as I would 
need to make several changes and need to do adequate testing of these changes,



Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia

Wolfgang Huber wrote:
> Hi Robert,
> my vote would be to leave them around for this release and .Defunct them 
> straight afterwards in the devel branch. We have 10 days until the 
> release schedule says "Deadline for packages passing R CMD check without 
> error". Many of the packages currently look quite good on the daily 
> check page. Some authors might now be away or busy during the next ten 
> days and it seems harsh to (possibly) impose making consequential 
> changes to their packages within that deadline.
> But I'll be happy to be convinced otherwise - progress is good and needs 
> to encouraged
>   Best wishes
> 	Wolfgang
>> Hi,
>>    I would like to get some comments on whether we can safely make all 
>> exprSet methods defunct, or of folks think we want yet one more cycle? 
>> I have found a few more lurking around recently, and I think it would 
>> help us to get them all expunged, sooner rather than later.
>>    thanks
>>     Robert
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