[BioC] AFFX-BioB-3_at annotation

[Ting-Yuan Liu]

Hi Xiwei,

Could you give us more detail about this?  I cannot reproduce your 
result:

> library(hgu133plus2)
> get("AFFX-BioB-3_at", hgu133plus2ACCNUM)
[1] "AFFX-BIOB-3"
> get("AFFX-BioB-3_at", hgu133plus2UNIGENE)
[1] NA
> library(mouse4302)
> get("AFFX-BioB-3_at", mouse4302UNIGENE)
[1] NA
> get("AFFX-BioB-3_at", mouse4302ACCNUM)
[1] "AFFX-BIOB-3"
> library(mouse430a2)
> get("AFFX-BioB-3_at", mouse430a2ACCNUM)
Error in get(x, envir, mode, inherits) : variable "AFFX-BioB-3_at" was not 
found
> sessionInfo()
Version 2.3.0 Under development (unstable) (2006-01-04 r36984) 
x86_64-unknown-linux-gnu 

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  
"grDevices"
[7] "utils"     "datasets"  "base"     

other attached packages:
 mouse430a2   mouse4302 hgu133plus2  AnnBuilder     RSQLite         DBI 
  "1.11.23"   "1.11.23"   "1.11.23"    "1.9.16"     "0.4-0"     "0.1-9" 

It seems that our developmental annotation packages don't have such 
mistakes.  Therefore, could you give us 
(1) the code you generate this mistake, and
(2) the output of sessionInfo()
so that we could have more information about your system?

Thanks,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Tue, 4 Apr 2006, Wu, Xiwei wrote:

> Dear list, 
>  
> It seems to me that no one has asked this question. In all of the
> annotation packages I looked at, including HGU133plus2, mouse4302,
> mouse430a2, AFFX-BioB-3_at are all annotated as FOS with a rat Unigene
> ID - Rn.103750. I thought it should be E coli bioB gene biotin
> synthetase. Am I missing sth here?
> 
> Xiwei Wu, MD, PhD 
> Director, Affymetrix Core Facility
> Research Scientist
> Department of Biomedical Informatics
> Beckman Research Institute
> City of Hope National Medical Center
> Duarte, CA 91010
> Phone: (626) 359-8111 ext. 65071
> 
> 
> "EMF <COH.ORG>" made the following annotations.
> ------------------------------------------------------------------------------
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