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}}

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}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Ting-Yuan, Thank you for your prompt reply. Here is the code and session information: > library(hgu133plus2) > get("AFFX-BioB-3_at", hgu133plus2ACCNUM) [1] "AFFX-BIOB-3" > get("AFFX-BioB-3_at", hgu133plus2UNIGENE) [1] "Rn.103750" > get("AFFX-BioB-3_at", hgu133plus2SYMBOL) [1] "Fos" > library(mouse4302) > get("AFFX-BioB-3_at", mouse4302ACCNUM) [1] "AFFX-BIOB-3" > get("AFFX-BioB-3_at", mouse4302UNIGENE) [1] "Rn.103750" > get("AFFX-BioB-3_at", mouse4302SYMBOL) [1] "Fos" > library(mouse430a2) > get("AFFX-BioB-3_at", mouse430a2ACCNUM) [1] "AFFX-BIOB-3" > get("AFFX-BioB-3_at", mouse430a2UNIGENE) [1] "Rn.103750" > get("AFFX-BioB-3_at", mouse430a2SYMBOL) [1] "Fos" > sessionInfo() R version 2.2.0, 2005-10-07, i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: mouse430a2 mouse4302 hgu133plus2 "1.10.0" "1.10.0" "1.10.0" 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. Xiwei -----Original Message----- From: Ting-Yuan Liu [mailto:tliu@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}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >