[BioC] Rat 230 2.0 annotation package

[James W. MacDonald]

David Kipling wrote:
> Hi
> 
> Although I can find the rae230a and rae230b rat annotation metadata 
> packages on the Bioconductor site, there doesn't seem to be one for the 
> rat 230 2.0 chip (which is the combination of rae230a and rae230b).

I see the rat2302 annotation package directly below the two you mention 
above (on the website).

Anyway, going to the website and downloading the package you want is 
probably the least efficient and most error prone way to do things. 
Please use the available functions in the reposTools package, which will 
automagically get the correct package for your particular version of R 
(not that critical here, but true in a general sense).

library(reposTools)
install.packages2("rat2302")

Will get you what you want.

Note that it is not always obvious what the name of the package will be, 
especially given Affy's complete inability to keep consistent naming 
standards. If you know the name that Affy has given the chip, then the 
package names are obvious; simply convert to lowercase and strip out any 
punctuation cruft that may be in the name (spaces, underscores, hyphens, 
dots, slashes, smiley faces... hey you never know with affy ;-D) e.g., 
the chip name in this case is the Rat 230_2, so the annotation package 
will be rat2302, the probe package will be rat2302probe, and the cdfenv 
will be rat2302cdf.

HTH,

Jim


> 
> Is one available anywhere, and if not what would be the easiest way to 
> make one (e.g. is is feasible to merge the two existing packages)?
> 
> Many thanks
> 
> David
> 
> Prof David Kipling
> Department of Pathology
> School of Medicine
> Cardiff University
> Heath Park
> Cardiff CF14 4XN
> 
> Tel:  029 2074 4847
> Email:  KiplingD at cardiff.ac.uk
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623