[Bioc-devel] Deprecation of xy2i and i2xy
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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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