Bioconductor package to map probe set ids from one chip to another chip
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Andrew Yee ▴ 350
@andrew-yee-2667
Last seen 7.3 years ago
This is a naive question, but is there a Bioconductor package that will map probe set ids from one chip to another chip? Thanks, Andrew [[alternative HTML version deleted]]
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.3 years ago
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Hi Andrew, I am really unsure about why you would want to do this, but if you did, you could grab the annotation packages for those two platforms and do something like this: library(hgu95av2.db) library(hgu133a.db) ##just to grab some real probesets for our example keys = Lkeys(hgu95av2ENTREZID)[100:200] ##now lets map 'em ##1st step is to get the entrez gene ID (which all of the human packages use as a central ID) EGs = mget(as.character(keys), hgu95av2ENTREZID, ifnotfound = NA) ##Then use the other package to the probes that go with those entrez gene IDs otherProbes = mget(as.character(EGs), revmap(hgu133aENTREZID), ifnotfound = NA) For this example I have assumed that you are trying to map between platforms of the same species. For different species that problem becomes a lot more challenging. Marc Andrew Yee wrote: > This is a naive question, but is there a Bioconductor package that will map > probe set ids from one chip to another chip? > Thanks, > Andrew > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >
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One more thing, I feel that I have to add an additional comment here. And that is to PLEASE be careful (with whatever it is that you have planned). In many cases the probesets in question may have been made to measure a completely different transcript on one platform than on another. So while we can definitely join them via their association with a particular gene in the way that I have shown you here, you could end up interpreting things very badly if you don't pay very careful attention to what they are actually meant to be sticking to. Marc Marc Carlson wrote: > Hi Andrew, > > I am really unsure about why you would want to do this, but if you did, > you could grab the annotation packages for those two platforms and do > something like this: > > library(hgu95av2.db) > library(hgu133a.db) > > ##just to grab some real probesets for our example > keys = Lkeys(hgu95av2ENTREZID)[100:200] > > ##now lets map 'em > ##1st step is to get the entrez gene ID (which all of the human packages > use as a central ID) > EGs = mget(as.character(keys), hgu95av2ENTREZID, ifnotfound = NA) > > ##Then use the other package to the probes that go with those entrez > gene IDs > otherProbes = mget(as.character(EGs), revmap(hgu133aENTREZID), > ifnotfound = NA) > > For this example I have assumed that you are trying to map between > platforms of the same species. For different species that problem > becomes a lot more challenging. > > > Marc > > > > > Andrew Yee wrote: > >> This is a naive question, but is there a Bioconductor package that will map >> probe set ids from one chip to another chip? >> Thanks, >> Andrew >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >> >> > > _______________________________________________ > 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 > >
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Although it's not in a Bioconductor package this mapping is provided in a series of text files from Affymetrix http://www.affymetrix.com/su pport/technical/comparison_spreadsheets.affx. For each pair of platforms compared you will find 3 files: best match, good match and complex. The spreadsheets compare probe sets using alignment of the representative sequences, alignment of PM probes to probe selection region, and alignment of PM probes to representative sequence. A detailed explanation is available in the user guide. I would also agree with Marc's comment that you need to be very careful that you understand what this mapping actually means. Gaye -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Marc Carlson Sent: Friday, April 24, 2009 12:11 PM To: Marc Carlson Cc: Andrew Yee; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Bioconductor package to map probe set ids from one chip to another chip One more thing, I feel that I have to add an additional comment here. And that is to PLEASE be careful (with whatever it is that you have planned). In many cases the probesets in question may have been made to measure a completely different transcript on one platform than on another. So while we can definitely join them via their association with a particular gene in the way that I have shown you here, you could end up interpreting things very badly if you don't pay very careful attention to what they are actually meant to be sticking to. Marc Marc Carlson wrote: > Hi Andrew, > > I am really unsure about why you would want to do this, but if you > did, you could grab the annotation packages for those two platforms > and do something like this: > > library(hgu95av2.db) > library(hgu133a.db) > > ##just to grab some real probesets for our example keys = > Lkeys(hgu95av2ENTREZID)[100:200] > > ##now lets map 'em > ##1st step is to get the entrez gene ID (which all of the human > packages use as a central ID) EGs = mget(as.character(keys), > hgu95av2ENTREZID, ifnotfound = NA) > > ##Then use the other package to the probes that go with those entrez > gene IDs otherProbes = mget(as.character(EGs), > revmap(hgu133aENTREZID), ifnotfound = NA) > > For this example I have assumed that you are trying to map between > platforms of the same species. For different species that problem > becomes a lot more challenging. > > > Marc > > > > > Andrew Yee wrote: > >> This is a naive question, but is there a Bioconductor package that >> will map probe set ids from one chip to another chip? >> Thanks, >> Andrew >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >> >> > > _______________________________________________ > 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 > > _______________________________________________ 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
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Thanks for the replies. My intent was to map from human to human, and for my purposes, using the Entrez ID as the common link as suggested in the replies is fine. However, I was also curious to if there was a package that would go beyond using the Entrez IDs to the level of sequence similarity between probe set IDs, etc. Thanks, Andrew On Fri, Apr 24, 2009 at 12:55 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi Andrew, > > I am really unsure about why you would want to do this, but if you did, > you could grab the annotation packages for those two platforms and do > something like this: > > library(hgu95av2.db) > library(hgu133a.db) > > ##just to grab some real probesets for our example > keys = Lkeys(hgu95av2ENTREZID)[100:200] > > ##now lets map 'em > ##1st step is to get the entrez gene ID (which all of the human packages > use as a central ID) > EGs = mget(as.character(keys), hgu95av2ENTREZID, ifnotfound = NA) > > ##Then use the other package to the probes that go with those entrez > gene IDs > otherProbes = mget(as.character(EGs), revmap(hgu133aENTREZID), > ifnotfound = NA) > > For this example I have assumed that you are trying to map between > platforms of the same species. For different species that problem > becomes a lot more challenging. > > > Marc > > > > > Andrew Yee wrote: > > This is a naive question, but is there a Bioconductor package that will > map > > probe set ids from one chip to another chip? > > Thanks, > > Andrew > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > [[alternative HTML version deleted]]
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Hi Andrew, The probe packages will furnish you with the actual sequences of the probes from the array platforms. Marc Andrew Yee wrote: > Thanks for the replies. My intent was to map from human to human, and > for my purposes, using the Entrez ID as the common link as suggested > in the replies is fine. However, I was also curious to if there was a > package that would go beyond using the Entrez IDs to the level of > sequence similarity between probe set IDs, etc. > > Thanks, > Andrew > > On Fri, Apr 24, 2009 at 12:55 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> <mailto:mcarlson at="" fhcrc.org="">> wrote: > > Hi Andrew, > > I am really unsure about why you would want to do this, but if you > did, > you could grab the annotation packages for those two platforms and do > something like this: > > library(hgu95av2.db) > library(hgu133a.db) > > ##just to grab some real probesets for our example > keys = Lkeys(hgu95av2ENTREZID)[100:200] > > ##now lets map 'em > ##1st step is to get the entrez gene ID (which all of the human > packages > use as a central ID) > EGs = mget(as.character(keys), hgu95av2ENTREZID, ifnotfound = NA) > > ##Then use the other package to the probes that go with those entrez > gene IDs > otherProbes = mget(as.character(EGs), revmap(hgu133aENTREZID), > ifnotfound = NA) > > For this example I have assumed that you are trying to map between > platforms of the same species. For different species that problem > becomes a lot more challenging. > > > Marc > > > > > Andrew Yee wrote: > > This is a naive question, but is there a Bioconductor package > that will map > > probe set ids from one chip to another chip? > > Thanks, > > Andrew > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > <mailto: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 > > > > > >
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