[Bioc-devel] Tiling array data

Rafael A Irizarry ririzarr at jhsph.edu
Wed Oct 18 21:57:20 CEST 2006

we are more than happy to support other techs. but we need help. 
basically it comes down to making the pdenv (the annotation package). it 
should not be too hard. we would love it if you volunteered to take care 
of agilent and  we will communicate with you to help you get it done. we 
are also ok with moving class defs to biobase, but as you guessed, it is 
still under devel.


Sean Davis wrote:
> On Wednesday 18 October 2006 12:55, Rafael A Irizarry wrote:
>> oligo has a class for tiling arrays.currently i use it to open affy and
>> nimblegen arrays.
> Thanks, Rafa.  I have looked at the oligo TilingFeatureSet.  The idea is to 
> pair the data with an annotation package, it seems?  Will it be difficult to 
> implement parsers and generate annotation packages for other array types like 
> agilent (just as an example)?  
> Is it possible and does it make sense to move TilingFeatureSet into Biobase to 
> reduce dependencies for folks who want to use it, as it does seem to offer a 
> general solution not specific to the oligo package?  If the consensus of the 
> developers is that TilingFeatureSet is the way to go, I would vote for doing 
> that (even if it isn't immediate, as I know that you and Benilton are still 
> actively developing Oligo).
> Sean

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