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

[Wolfgang Huber]

Hi Jim,

I think Francesco's point is valid.
The chip design is independent of particular instances of data, and
includes the size of the chip. That the chip size resides in the data
container (AffyBatch) and all the other geometry annotation in the CDF
is incoherent. So, when the i2xy and xy2i functions go, can't we have
this annotation constant defined in the CDF package as well, so that you
can say, for example

  xy <- indices2xy(i, cdf=hgu133acdf)

Btw, the reason for putting the xy2i and i2xy functions into the CDF
packages was that these mapping functions are really a chip-geometry
annotation. It was a mistake to export them like that, though, they
should always only have been visible as hgu133acdf::xy2i() or
hgu133acdf$xy2i().

  Best wishes
  Wolfgang


> Hi Francesco,
> 
> Francesco Ferrari wrote:
>> PS: I know that no package uses these functions, but we use them to
>> produce data for another package (work is still in progress). We could
>> use indices2xy() and xy2indices() functions from affy package, but the
>> value for "nr" parameter is required.
> 
> I'm confused by this. What does your package do with a cdf package that 
> doesn't explicitly involve an AffyBatch?
> 
> Best,
> 
> Jim