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

James W. MacDonald jmacdon at med.umich.edu
Mon Mar 26 17:41:14 CEST 2007

Hi Wolfgang,

Wolfgang Huber wrote:
> Hi Jim,
> I think Francesco's point is valid.

I agree. I wasn't intending to imply that it wasn't - I just don't know 
what one would do with cdf information that didn't involve some Affy 
data, and wondered what I was missing.

> 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)

That sounds reasonable, and should be simple to do.



> 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?

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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