mouse4302.db and can't find gene symbol annotation
1
0
Entering edit mode
Andrew Yee ▴ 350
@andrew-yee-2667
Last seen 7.3 years ago
I know I've raised a similar issue in May 2009 concerning how frequently the annotation packages are updated, and I imagine this issue has been raised by others as well: For this probe set id, 1449880_s_at, I am having some difficulty finding annotation information for it in the mouse4302.db. The Affymerix website has its gene symbol annotation as Bglap, and the date of their annotation file is from July 2011 https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=MOUSE43 0_2:1449880_S_AT#a_grade However, I can't seem to find a similar annotation in the mouse4302.db annotation package. I was wondering if there was a simple explanation for this, or perhaps I am doing something wrong. Thanks, Andrew sessionInfo() R version 2.15.0 Patched (2012-03-30 r58877) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302.db_2.7.1 org.Mm.eg.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 [5] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] IRanges_1.14.2 stats4_2.15.0 tools_2.15.0
Annotation mouse4302 probe Annotation mouse4302 probe • 809 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 11 hours ago
United States
Hi Andrew, On 10/22/2012 10:58 PM, Andrew Yee wrote: > I know I've raised a similar issue in May 2009 concerning how > frequently the annotation packages are updated, and I imagine this > issue has been raised by others as well: > > For this probe set id, 1449880_s_at, I am having some difficulty > finding annotation information for it in the mouse4302.db. > > The Affymerix website has its gene symbol annotation as Bglap, and the > date of their annotation file is from July 2011 > > https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=MOUSE 430_2:1449880_S_AT#a_grade > > However, I can't seem to find a similar annotation in the mouse4302.db > annotation package. I was wondering if there was a simple explanation > for this, or perhaps I am doing something wrong. It's a simple explanation. This probeset targets multiple genes, and the default of the annotation packages is to only return data for probesets that target a single gene. This behavior is modifiable, however. What you have been getting is this: > get("1449880_s_at", mouse4302SYMBOL) [1] NA but we can allow multiple hits using toggleProbes(): > x <- toggleProbes(mouse4302SYMBOL, "multiple") > get("1449880_s_at", x) [1] "Bglap" "Bglap-rs1" "Bglap2" Best, Jim > > Thanks, > Andrew > > sessionInfo() > > R version 2.15.0 Patched (2012-03-30 r58877) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mouse4302.db_2.7.1 org.Mm.eg.db_2.7.1 RSQLite_0.11.1 > DBI_0.2-5 > [5] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 > BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] IRanges_1.14.2 stats4_2.15.0 tools_2.15.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENT
0
Entering edit mode
Thanks for the information, that's extremely helpful. Thanks, Andrew On Tue, Oct 23, 2012 at 10:43 AM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi Andrew, > > > On 10/22/2012 10:58 PM, Andrew Yee wrote: >> >> I know I've raised a similar issue in May 2009 concerning how >> frequently the annotation packages are updated, and I imagine this >> issue has been raised by others as well: >> >> For this probe set id, 1449880_s_at, I am having some difficulty >> finding annotation information for it in the mouse4302.db. >> >> The Affymerix website has its gene symbol annotation as Bglap, and the >> date of their annotation file is from July 2011 >> >> >> https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=MOUS E430_2:1449880_S_AT#a_grade >> >> However, I can't seem to find a similar annotation in the mouse4302.db >> annotation package. I was wondering if there was a simple explanation >> for this, or perhaps I am doing something wrong. > > > It's a simple explanation. This probeset targets multiple genes, and the > default of the annotation packages is to only return data for probesets that > target a single gene. This behavior is modifiable, however. > > What you have been getting is this: > >> get("1449880_s_at", mouse4302SYMBOL) > [1] NA > > but we can allow multiple hits using toggleProbes(): > >> x <- toggleProbes(mouse4302SYMBOL, "multiple") >> get("1449880_s_at", x) > [1] "Bglap" "Bglap-rs1" "Bglap2" > > Best, > > Jim > > > >> >> Thanks, >> Andrew >> >> sessionInfo() >> >> R version 2.15.0 Patched (2012-03-30 r58877) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] mouse4302.db_2.7.1 org.Mm.eg.db_2.7.1 RSQLite_0.11.1 >> DBI_0.2-5 >> [5] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >> BiocInstaller_1.4.3 >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.14.2 stats4_2.15.0 tools_2.15.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 >
ADD REPLY
0
Entering edit mode
Hi Andrew, You can also just get your symbols this way: library(mouse4302.db) library(org.Mm.eg.db) select( mouse4302.db, keys ="1449880_s_at", cols="SYMBOL", keytype="PROBEID") This query will give you a warning because your probe will match to multiple symbols, but it avoids the step of having to create a special bimap that is set to expose all probes 1st. Marc On 10/23/2012 09:06 AM, Andrew Yee wrote: > Thanks for the information, that's extremely helpful. > > Thanks, > Andrew > > On Tue, Oct 23, 2012 at 10:43 AM, James W. MacDonald<jmacdon at="" uw.edu=""> wrote: >> Hi Andrew, >> >> >> On 10/22/2012 10:58 PM, Andrew Yee wrote: >>> I know I've raised a similar issue in May 2009 concerning how >>> frequently the annotation packages are updated, and I imagine this >>> issue has been raised by others as well: >>> >>> For this probe set id, 1449880_s_at, I am having some difficulty >>> finding annotation information for it in the mouse4302.db. >>> >>> The Affymerix website has its gene symbol annotation as Bglap, and the >>> date of their annotation file is from July 2011 >>> >>> >>> https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=MOU SE430_2:1449880_S_AT#a_grade >>> >>> However, I can't seem to find a similar annotation in the mouse4302.db >>> annotation package. I was wondering if there was a simple explanation >>> for this, or perhaps I am doing something wrong. >> >> It's a simple explanation. This probeset targets multiple genes, and the >> default of the annotation packages is to only return data for probesets that >> target a single gene. This behavior is modifiable, however. >> >> What you have been getting is this: >> >>> get("1449880_s_at", mouse4302SYMBOL) >> [1] NA >> >> but we can allow multiple hits using toggleProbes(): >> >>> x<- toggleProbes(mouse4302SYMBOL, "multiple") >>> get("1449880_s_at", x) >> [1] "Bglap" "Bglap-rs1" "Bglap2" >> >> Best, >> >> Jim >> >> >> >>> Thanks, >>> Andrew >>> >>> sessionInfo() >>> >>> R version 2.15.0 Patched (2012-03-30 r58877) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] mouse4302.db_2.7.1 org.Mm.eg.db_2.7.1 RSQLite_0.11.1 >>> DBI_0.2-5 >>> [5] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>> BiocInstaller_1.4.3 >>> >>> loaded via a namespace (and not attached): >>> [1] IRanges_1.14.2 stats4_2.15.0 tools_2.15.0 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >>
ADD REPLY

Login before adding your answer.

Traffic: 240 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6