[BioC] misnamed annotation environments with annaffy

[James W. MacDonald]

Jacob Michaelson wrote:
> Hi all,
> 
> Several months ago I built a custom annotation package for Affy's  Yeast 
> 2.0 chip.  Both I and the function I used gave some  inconvenient names 
> to the environments within the package and I've  had some problems with 
> annaffy because of it.
> 
> My problem:
> 
> An environment named "YEAST2GENENAMES" contains information normally  
> found by annaffy under the "SYMBOL" label.
> 
> An environment named "YEAST2DESCRIPTION" contains information  normally 
> found by annaffy under the "GENENAMES" label.
> 
> The result of this is that nothing from DESCRIPTION is displayed (to  my 
> knowledge, annaffy doesn't handle DESCRIPTIONs), and the  information in 
> GENENAMES is displayed in the wrong place.
> 
> Where do I need to do the renaming and can I do it with the package  
> already built?

Look at the function aaf.handler() as well as aafSymbol() and 
aafDescription(). You should be able to make the necessary changes in 
these three functions to do what you want.

You can make these changes using a built package, but the changes will 
be transient. Simply load the package, then source your modified 
functions. This will mask the existing functions for the current 
session. If you want more permanent changes, you will have to modify the 
source package and re-build.

HTH,

Jim


> 
> Thanks in advance,
> 
> Jake
> 
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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
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