[Bioc-devel] Deprecation of xy2i and i2xy

James MacDonald jmacdon at med.umich.edu
Thu Apr 12 19:43:09 CEST 2007


I just committed changes to both makecdfenv and affy that complete the first step in deprecation of the xy2i and i2xy functions.

In BioC 2.0, all cdf packages will have a second env, named e.g., hgu133plus2dim that will contain two key-value pairs, the keys being 'NROW' and "NCOL'.

The indices2xy() and xy2indices() functions now have an additional argument 'cdf' that is the character name of the cdf package to use to get this information if you don't have an AffyBatch. 

For example:

> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio
> xy2indices(50,324, cdf="agcdf")
[1] 173067
> indices2xy(173067, cdf="agcdf")
      x   y
[1,] 50 324
> xy2i(50, 324)
[1] 173067
Warning message:
xy2i is deprecated and will be removed in the next BioC release.
Use xy2indices in the affy package instead. 
> i2xy(173067)
      x   y
[1,] 50 324
Warning message:
i2xy is deprecated and will be removed in the next BioC release.
Use indices2xy in the affy package instead.

Note that the agcdf package I used here is one I just built, so this won't work with any of the cdf packages currently in the BioC devel repository. I will be rebuilding the packages Real Soon Now and they will definitely be part of the 2.0 release.




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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