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

Francesco Ferrari ferrari.francesco at unimore.it
Mon Mar 26 20:22:27 CEST 2007

Sorry, I didn't report many details since, as I wrote, the work is
still in progress. However our functions will not be included into a
novel package.
Our functions retrieve information concerning x/y coordinates of PM
and MM probes. PM probes coordinates can also be obtained from probe
packages (such as hgu133aprobe package) but MM probes coordinates are
stored only in CDF packages, and chip geometry information are
required to convert CDF package data to x/y coordinates.
These data are then stored for subsequent use with a specific
AffyBatch, but the retrieved information are independent of a specific
AffyBatch object.

Best regards,

On 3/26/07, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> 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
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
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