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
>
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}}
> >
> > _______________________________________________
> > 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
> >
>
>
>