[Bioc-devel] RFC: xy2i and i2xy in *cdf packages

James W. MacDonald jmacdon at med.umich.edu
Wed Apr 11 22:53:55 CEST 2007

Seth Falcon wrote:
> Wolfgang Huber <huber at ebi.ac.uk> writes:
>>Rather than make up these new dimension objects in the CDF package,
>>why not teach the affy:indices2xy function to reach into the
>>appropriate CDF package and grab the *unexported*, existing i2xy
>>function in order to do its thing, and the affy:xy2indices to grab the
>>*unexported* xy2i function? Seems like the least intrusive way to do
>>things, and more flexible.
> I don't think we should change the visibility of the xy2i functions
> without going through the deprecation cycle.
> But in general, I like your suggestion.  Teaching affy to grab the
> appropriate function seems sensible.  Personally, I think it is fine
> to have these functions exported.  You can still get the right one
> when using affy::xy2indices.  Symbol masking is a fact of R.
> But having the dimensions accessible in the CDF package also makes
> sense to me and is easy so I'm still in favor of adding hgu95av2dim.
> And the xy2i and i2xy functions should use it...

The functions in affy don't care what happens with xy2i and i2xy since 
they don't use them (they get dimensions directly from the AffyBatch). 
The only functions that care are those that don't have an AffyBatch to 

So, unless there are any objections*, I will add the little dim env to 
the cdf packages any any functions that need this info (and don't have 
an AffyBatch to query) will have to learn to use it.

*By objections, I mean 'This will completely break my code and destroy 
my life'. The cdf packages are nearing the end of their shelf lives, 
soon to be replaced with SQLite packages, so arguments about stylistic 
differences and 'How things should be done' are counterproductive, 
especially given how close we are to release. Also, remember that xy2i 
and i2xy are only being _deprecated_. Anybody who uses these functions 
has > 6 months from now to make changes.



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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