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Question: affymetrix annotation
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gravatar for arne.mueller@novartis.com
7.8 years ago by
Switzerland
Hello, I was wondering where the mapping from affy probeset Ids to genes (EntrezGene) is coming from (package mouse4302.db). mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, what's the "original" link between an affy probeset and an EnterzGene Id, is it Netaffx? My problem is that I've an "interesting" probeset that is annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map contains NA for this probeset Id. I'd be happy if someone could point me to some documentation how this annotation/mapping is derived or let me know what I'm doing wrong ...? thanks a lot for your help, arne [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.8 years ago by Tim Yates250 • written 7.8 years ago by arne.mueller@novartis.com200
0
gravatar for James W. MacDonald
7.8 years ago by
United States
James W. MacDonald48k wrote:
Hi Arne, On 12/20/2010 11:26 AM, arne.mueller at novartis.com wrote: > Hello, > > I was wondering where the mapping from affy probeset Ids to genes > (EntrezGene) is coming from (package mouse4302.db). > mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, > what's the "original" link between an affy probeset and an EnterzGene Id, > is it Netaffx? My problem is that I've an "interesting" probeset that is > annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map > contains NA for this probeset Id. > > I'd be happy if someone could point me to some documentation how this > annotation/mapping is derived or let me know what I'm doing wrong ...? I doubt you are doing anything wrong. This may have changed a bit from the last time I talked to Marc, but in the past we needed a 'primary' mapping to start with, and chose the Affymetrix probeset ID --> Entrez Gene mapping that you can get from the latest Affy annotation file. We assumed this to be the truth, and then did all the other mappings from Entrez Gene. The problem with this is that we are by definition using more dated information than you will typically get from Netaffx. So it is quite likely, given the fluid nature of this field, that some probesets will have different data in Netaffx than what you can get from the annotation packages. As an aside, does this probeset have an Entrez Gene ID in the annotation package? Best, Jim > > thanks a lot for your help, > > arne > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 7.8 years ago by James W. MacDonald48k
Hello, thanks Jim for your reply. The org.Mm.eg.db::org.Mm.egSYMBOL has the gene symbol for the probeset of interest, it's just mouse4302 that's missing it. I've just checked in an older netffx annotation files (older than 2007, 2009, and the current one from 2010). The probeset was annotated already in 2007, but it was always assigned to two Entrez Gene Ids: 100047700 /// 13094, the 2nd one seems to be the correct Id and the first one was removed from entrez gene Oct 28th 2010 (flagged "withdrawn"). Note that the first Id is the withdrawn one ... If the bioc annotation pipeline comes across ambiguous annotation, that it cannot resolve, does it ignore the annotation (since there is no unique gene Id available), and therefore sets the entrez gene id to NA? Note, the gene id in entrez gene was flagged "withdrawn" in October this year, and the date of the Entrez used in mouse4032 is September 2010 (i.e. the entry was still valid in entrez gene - and therefore ambiguous ...). I'm asking because I found I found this gene interesting form some reason and it was annotated as Cyp2b9 in our gene expressino software (using netaffx) but not annotated at all in one of my post-processing pipelines that uses the mouse4302.db from bioc. kind regards, Arne ps: the probeset I'm talking about is 1419590_at "James W. MacDonald" <jmacdon@med.umich.edu> 12/20/2010 09:58 PM To arne.mueller@novartis.com cc bioconductor@stat.math.ethz.ch Subject Re: [BioC] affymetrix annotation Hi Arne, On 12/20/2010 11:26 AM, arne.mueller@novartis.com wrote: > Hello, > > I was wondering where the mapping from affy probeset Ids to genes > (EntrezGene) is coming from (package mouse4302.db). > mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, > what's the "original" link between an affy probeset and an EnterzGene Id, > is it Netaffx? My problem is that I've an "interesting" probeset that is > annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map > contains NA for this probeset Id. > > I'd be happy if someone could point me to some documentation how this > annotation/mapping is derived or let me know what I'm doing wrong ...? I doubt you are doing anything wrong. This may have changed a bit from the last time I talked to Marc, but in the past we needed a 'primary' mapping to start with, and chose the Affymetrix probeset ID --> Entrez Gene mapping that you can get from the latest Affy annotation file. We assumed this to be the truth, and then did all the other mappings from Entrez Gene. The problem with this is that we are by definition using more dated information than you will typically get from Netaffx. So it is quite likely, given the fluid nature of this field, that some probesets will have different data in Netaffx than what you can get from the annotation packages. As an aside, does this probeset have an Entrez Gene ID in the annotation package? Best, Jim > > thanks a lot for your help, > > arne > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues [[alternative HTML version deleted]]
ADD REPLYlink written 7.8 years ago by arne.mueller@novartis.com200
Hi Arne, Aha! I didn't know there were two IDs associated with this probeset (although I should have thought of that, or you know, looked it up...my bad). So, here's the deal. When there are multiple IDs associated with a given probeset, it is difficult to say which one is correct. Or put another way, it is difficult to know exactly what the probeset is actually measuring. In the past, what we did was take the first Entrez Gene ID as the correct one, and ignore the rest. This of course is suboptimal, as we are ignoring information. Recently, we decided to mask these questionable mappings, and only expose the mappings that have unique probeset --> Entrez Gene mappings, but also give a way for people to get all the questionable mappings as well. If you want to see all the one-to-many mappings, you can use the infamous toggleProbes() function thusly: > suppressMessages(library(mouse4302.db)) > a <- "1419590_at" > z <- toggleProbes(mouse4302ENTREZID, "all") > get(a,z) [1] "100047700" "13094" > q <- toggleProbes(mouse4302SYMBOL, "all") > get(a,q) [1] "LOC100047700" "Cyp2b9" Best, Jim On 12/21/2010 6:15 AM, arne.mueller at novartis.com wrote: > Hello, > > thanks Jim for your reply. The org.Mm.eg.db::org.Mm.egSYMBOL has the gene > symbol for the probeset of interest, it's just mouse4302 that's missing > it. > > I've just checked in an older netffx annotation files (older than 2007, > 2009, and the current one from 2010). The probeset was annotated already > in 2007, but it was always assigned to two Entrez Gene Ids: 100047700 /// > 13094, the 2nd one seems to be the correct Id and the first one was > removed from entrez gene Oct 28th 2010 (flagged "withdrawn"). Note that > the first Id is the withdrawn one ... If the bioc annotation pipeline > comes across ambiguous annotation, that it cannot resolve, does it ignore > the annotation (since there is no unique gene Id available), and therefore > sets the entrez gene id to NA? > > Note, the gene id in entrez gene was flagged "withdrawn" in October this > year, and the date of the Entrez used in mouse4032 is September 2010 (i.e. > the entry was still valid in entrez gene - and therefore ambiguous ...). > > I'm asking because I found I found this gene interesting form some reason > and it was annotated as Cyp2b9 in our gene expressino software (using > netaffx) but not annotated at all in one of my post-processing pipelines > that uses the mouse4302.db from bioc. > > kind regards, > > Arne > > ps: the probeset I'm talking about is 1419590_at > > > > > "James W. MacDonald"<jmacdon at="" med.umich.edu=""> > 12/20/2010 09:58 PM > > To > arne.mueller at novartis.com > cc > bioconductor at stat.math.ethz.ch > Subject > Re: [BioC] affymetrix annotation > > > > > > > Hi Arne, > > On 12/20/2010 11:26 AM, arne.mueller at novartis.com wrote: >> Hello, >> >> I was wondering where the mapping from affy probeset Ids to genes >> (EntrezGene) is coming from (package mouse4302.db). >> mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, >> what's the "original" link between an affy probeset and an EnterzGene > Id, >> is it Netaffx? My problem is that I've an "interesting" probeset that is >> annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map >> contains NA for this probeset Id. >> >> I'd be happy if someone could point me to some documentation how this >> annotation/mapping is derived or let me know what I'm doing wrong ...? > > I doubt you are doing anything wrong. This may have changed a bit from > the last time I talked to Marc, but in the past we needed a 'primary' > mapping to start with, and chose the Affymetrix probeset ID --> Entrez > Gene mapping that you can get from the latest Affy annotation file. > > We assumed this to be the truth, and then did all the other mappings > from Entrez Gene. The problem with this is that we are by definition > using more dated information than you will typically get from Netaffx. > So it is quite likely, given the fluid nature of this field, that some > probesets will have different data in Netaffx than what you can get from > the annotation packages. > > As an aside, does this probeset have an Entrez Gene ID in the annotation > package? > > Best, > > Jim > > > > >> >> thanks a lot for your help, >> >> arne >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD REPLYlink written 7.8 years ago by James W. MacDonald48k
0
gravatar for Cristobal Fresno Rodríguez
7.8 years ago by
Argentina/Cordoba/Universidad Católica de Córdoba (CONICET)
Hi there, The last updated annotation is at affymetrix website and download it. Hope it works for you. Kachelo 2010/12/20 <arne.mueller@novartis.com> > Hello, > > I was wondering where the mapping from affy probeset Ids to genes > (EntrezGene) is coming from (package mouse4302.db). > mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, > what's the "original" link between an affy probeset and an EnterzGene Id, > is it Netaffx? My problem is that I've an "interesting" probeset that is > annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map > contains NA for this probeset Id. > > I'd be happy if someone could point me to some documentation how this > annotation/mapping is derived or let me know what I'm doing wrong ...? > > thanks a lot for your help, > > arne > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.8 years ago by Cristobal Fresno Rodríguez360
0
gravatar for Tim Yates
7.8 years ago by
Tim Yates250
Tim Yates250 wrote:
We map to the Ensembl genome, so it's probably not what you are after, but we have the 430A arrays in xmap and you can search for probesets by entering their ids into the search box top right http://xmap.picr.man.ac.uk/?s=mus_musculus&v=60&a=Mouse430A_2 How it's of some help... Tim ----- Reply message ----- From: "arne.mueller@novartis.com" <arne.mueller@novartis.com> Date: Mon, Dec 20, 2010 16:32 Subject: [BioC] affymetrix annotation To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> Hello, I was wondering where the mapping from affy probeset Ids to genes (EntrezGene) is coming from (package mouse4302.db). mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, what's the "original" link between an affy probeset and an EnterzGene Id, is it Netaffx? My problem is that I've an "interesting" probeset that is annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map contains NA for this probeset Id. I'd be happy if someone could point me to some documentation how this annotation/mapping is derived or let me know what I'm doing wrong ...? thanks a lot for your help, arne [[alternative HTML version deleted]] _______________________________________________ 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 -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}
ADD COMMENTlink written 7.8 years ago by Tim Yates250
0
gravatar for Tim Yates
7.8 years ago by
Tim Yates250
Tim Yates250 wrote:
Hiya! Glad you like it! There is the xmapbridge bioconductor package which (in partnership with the xmapbridge application downloadable from the xmap site) can be used to draw your own plots over the top of xmap. tim ----- Reply message ----- From: "arne.mueller@novartis.com" <arne.mueller@novartis.com> Date: Tue, Dec 21, 2010 12:02 Subject: [BioC] affymetrix annotation To: "Tim Yates" <tyates at="" picr.man.ac.uk=""> Hi Tim, Thanks for the link, this is a great tool - easy to see/test if probes are located in exons, cool! Is it possible to upload custom tracks (like in ucsc) or would I need to run xmap on my own web-server? thanks a lot for this link, Arne "Tim Yates" <tyates at="" picr.man.ac.uk=""> 12/20/2010 10:29 PM To <arne.mueller at="" novartis.com="">, <bioconductor at="" stat.math.ethz.ch=""> cc Subject Re: [BioC] affymetrix annotation We map to the Ensembl genome, so it's probably not what you are after, but we have the 430A arrays in xmap and you can search for probesets by entering their ids into the search box top right http://xmap.picr.man.ac.uk/?s=mus_musculus&v=60&a=Mouse430A_2 How it's of some help... Tim ----- Reply message ----- From: "arne.mueller@novartis.com" <arne.mueller@novartis.com> Date: Mon, Dec 20, 2010 16:32 Subject: [BioC] affymetrix annotation To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> Hello, I was wondering where the mapping from affy probeset Ids to genes (EntrezGene) is coming from (package mouse4302.db). mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, what's the "original" link between an affy probeset and an EnterzGene Id, is it Netaffx? My problem is that I've an "interesting" probeset that is annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map contains NA for this probeset Id. I'd be happy if someone could point me to some documentation how this annotation/mapping is derived or let me know what I'm doing wrong ...? thanks a lot for your help, arne [[alternative HTML version deleted]] _______________________________________________ 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 -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:28}}
ADD COMMENTlink written 7.8 years ago by Tim Yates250
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