[Bioc-devel] Deprecation of xy2i and i2xy

[Henrik Bengtsson]

Hi,

thanks for this.

Just a thought, would it be much work to also add a "chipType" value
to containing the name of the original chip type.  Right now it is not
possible to identify the original chip type given the package (or
"clean" CDF name) - the mapping is in one direction only.  Example:

> cleancdfname("Mapping250K_Nsp")
[1] "mapping250knspcdf"'

> chipType("mapping250knspcdf")
[1] "Mapping250K_Nsp"

which would be handy when for instance looking up additional external
annotation data/files given the CDF package etc.

Cheers

Henrik

On 4/12/07, James MacDonald <jmacdon at med.umich.edu> wrote:
> Hi,
>
> 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.
>
> 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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