[BioC] AFFX-BioB-3_at annotation

[Ting-Yuan Liu]

On Wed, 5 Apr 2006, Wu, Xiwei wrote:

> Apparently, I am using the stable release BIOC1.7 annotation packages.
> It seems that the problem is fixed in the developmental packages. Why
> this probeset is not found in the developmental mouse430a2? It should be
> there on the chip.

It seems that Affymetrix found this bug and fixed it already so that our 
developmental packages don't have the same bug.  

I just find a tiny bug in the mouse430a2 basefiles, and I will rebuild 
mouse430a2 today.  You shouldn't see the bug any more.  Good catch.

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

> 
> Xiwei
> 
> -----Original Message-----
> From: Ting-Yuan Liu [mailto:tliu at fhcrc.org] 
> Sent: Tuesday, April 04, 2006 6:11 PM
> To: Wu, Xiwei
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] AFFX-BioB-3_at annotation
> 
> 
> 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.
> > ----------------------------------------------------------------------
> > -------- SECURITY/CONFIDENTIALITY WARNING:  This message and any 
> > atta...{{dropped}}
> > 
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> 
> 
>