Fwd: How to handle the case a Affymetrix probe set ID mapped to multiple genes?

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Levi Waldron ★ 1.1k

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CUNY Graduate School of Public Health a…

On Tue, Jul 30, 2013 at 9:14 AM, Feng Tian <fengtian@bu.edu> wrote: > Hi Levi, > > Thanks for your reply very much. > My purpose is to do GSEA analysis. So is there a general way to handle > these "_x" probes? > > Regards, > Feng > After mapping, I would just drop anything with "///" for GSEA analysis. I suppose you could also choose one representative, or if you are using the Broad's tool, provide probe sets and let it deal with the mapping (although I don't know how it deals with non-specific probe sets). I doubt such probe sets will have much effect on GSEA results, since most of those genes will have a more specific probeset available. E.g.: > library(hgu133plus2.db) > x=as.character(hgu133plus2SYMBOL) > length(x) [1] 41293 #probe sets > length(unique(x)) [1] 19944 #gene symbols > ind=grep("_x", names(x)) > summary(x[ind] %in% x[-ind]) Mode FALSE TRUE NA's logical 623 2469 0 > So for hgu133plus2 you would lose 623 out of 19944 genes - IMO if that changes your GSEA in an important way, it probably wasn't a robust result anyways. > > On Tue, Jul 30, 2013 at 9:00 AM, Levi Waldron <lwaldron.research@gmail.com> > wrote: > >> Hi Feng, >> >> probe sets labelled with "_x" cross-hybridize to multiple genes: >> >> http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.jsp >> >> Genecards gives more detail for this probe set: >> >> >> http://genecards.weizmann.ac.il/cgi-bin/geneannot/GA_search.pl?keyw ord_type=probe_set_id&array=HG-U133&target=genecards&keyword=200012_x_ at >> >> How to handle such a case depends on how interested you are in that probe >> set; at the extremes you could ignore it, or follow up with PCR to >> establish which transcript you are observing. >> >> -Levi >> >> >> On Mon, Jul 29, 2013 at 6:06 PM, Feng Tian <fengtian@bu.edu> wrote: >> >> > Dear all, >> > >> > In the Affymetrix annotation file, I find that some probe set ID are >> mapped >> > to multiple genes separated by '///', such as 200012_x_at is mapped >> > to RPL21P16///RPL21P119///RPL21. How to handle this case? >> > >> > Thank you! >> > >> > Feng >> > >> > [[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 >> > >> >> >> >> -- >> Levi Waldron >> Post-doctoral fellow >> Department of Biostatistics, Harvard School of Public Health >> Department of Biostatistics and Computational Biology, Dana-Farber Cancer >> Institute >> Building 1, room 412C >> 655 Huntington Avenue >> Boston, Massachusetts 02115 >> mobile: (617) 851-6849 >> fax: (617) 432-5619 >> http://www.hsph.harvard.edu/research/levi-waldron/ >> >> [[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]]

Annotation hgu133plus2 probe Annotation hgu133plus2 probe • 1.8k views

ADD COMMENT • link updated 11.3 years ago by Yuan Hao ▴ 240 • written 11.3 years ago by Levi Waldron ★ 1.1k

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Yuan Hao ▴ 240

@yuan-hao-3658

Last seen 10.2 years ago

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GSEA mostly uses entrez gene ids during test. Most "_x" probe sets eventually won't have corresponding entrez ids mapped to, which would be automatically excluded before the test, so they shouldn't be a problem for you. Cheers, Yuan On Jul 30, 2013, at 9:43 AM, Levi Waldron <lwaldron.research at="" gmail.com=""> wrote: > On Tue, Jul 30, 2013 at 9:14 AM, Feng Tian <fengtian at="" bu.edu=""> wrote: > >> Hi Levi, >> >> Thanks for your reply very much. >> My purpose is to do GSEA analysis. So is there a general way to handle >> these "_x" probes? >> >> Regards, >> Feng >> > > After mapping, I would just drop anything with "///" for GSEA analysis. I > suppose you could also choose one representative, or if you are using the > Broad's tool, provide probe sets and let it deal with the mapping (although > I don't know how it deals with non-specific probe sets). I doubt such > probe sets will have much effect on GSEA results, since most of those genes > will have a more specific probeset available. E.g.: > >> library(hgu133plus2.db) >> x=as.character(hgu133plus2SYMBOL) >> length(x) > [1] 41293 #probe sets >> length(unique(x)) > [1] 19944 #gene symbols >> ind=grep("_x", names(x)) >> summary(x[ind] %in% x[-ind]) > Mode FALSE TRUE NA's > logical 623 2469 0 >> > > So for hgu133plus2 you would lose 623 out of 19944 genes - IMO if that > changes your GSEA in an important way, it probably wasn't a robust result > anyways. > > > > > > >> >> On Tue, Jul 30, 2013 at 9:00 AM, Levi Waldron <lwaldron.research at="" gmail.com="">>> wrote: >> >>> Hi Feng, >>> >>> probe sets labelled with "_x" cross-hybridize to multiple genes: >>> >>> http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.jsp >>> >>> Genecards gives more detail for this probe set: >>> >>> >>> http://genecards.weizmann.ac.il/cgi-bin/geneannot/GA_search.pl?key word_type=probe_set_id&array=HG-U133&target=genecards&keyword=200012_x _at >>> >>> How to handle such a case depends on how interested you are in that probe >>> set; at the extremes you could ignore it, or follow up with PCR to >>> establish which transcript you are observing. >>> >>> -Levi >>> >>> >>> On Mon, Jul 29, 2013 at 6:06 PM, Feng Tian <fengtian at="" bu.edu=""> wrote: >>> >>>> Dear all, >>>> >>>> In the Affymetrix annotation file, I find that some probe set ID are >>> mapped >>>> to multiple genes separated by '///', such as 200012_x_at is mapped >>>> to RPL21P16///RPL21P119///RPL21. How to handle this case? >>>> >>>> Thank you! >>>> >>>> Feng >>>> >>>> [[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 >>>> >>> >>> >>> >>> -- >>> Levi Waldron >>> Post-doctoral fellow >>> Department of Biostatistics, Harvard School of Public Health >>> Department of Biostatistics and Computational Biology, Dana-Farber Cancer >>> Institute >>> Building 1, room 412C >>> 655 Huntington Avenue >>> Boston, Massachusetts 02115 >>> mobile: (617) 851-6849 >>> fax: (617) 432-5619 >>> http://www.hsph.harvard.edu/research/levi-waldron/ >>> >>> [[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 >>> >> >> > > [[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

ADD COMMENT • link 11.3 years ago Yuan Hao ▴ 240

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On Tue, Jul 30, 2013 at 11:07 AM, Yuan Hao <yuan.x.hao@gmail.com> wrote: > GSEA mostly uses entrez gene ids during test. Most "_x" probe sets > eventually won't have corresponding entrez ids mapped to, which would be > automatically excluded before the test, so they shouldn't be a problem for > you. > > Cheers, > Yuan > I think the number of excluded genes is the same whether you use symbols or Entrez IDs: > library(hgu133plus2.db) > x=as.character(hgu133plus2ENTREZID) > length(x) [1] 41293 > length(unique(x)) [1] 19944 > ind=grep("_x", names(x)) > summary(x[ind] %in% x[-ind]) Mode FALSE TRUE NA's logical 623 2469 0 > head(x) 1053_at 117_at 121_at 1255_g_at 1294_at 1316_at "5982" "3310" "7849" "2978" "7318" "7067" > > On Jul 30, 2013, at 9:43 AM, Levi Waldron <lwaldron.research@gmail.com> > wrote: > > > On Tue, Jul 30, 2013 at 9:14 AM, Feng Tian <fengtian@bu.edu> wrote: > > > >> Hi Levi, > >> > >> Thanks for your reply very much. > >> My purpose is to do GSEA analysis. So is there a general way to handle > >> these "_x" probes? > >> > >> Regards, > >> Feng > >> > > > > After mapping, I would just drop anything with "///" for GSEA analysis. I > > suppose you could also choose one representative, or if you are using the > > Broad's tool, provide probe sets and let it deal with the mapping > (although > > I don't know how it deals with non-specific probe sets). I doubt such > > probe sets will have much effect on GSEA results, since most of those > genes > > will have a more specific probeset available. E.g.: > > > >> library(hgu133plus2.db) > >> x=as.character(hgu133plus2SYMBOL) > >> length(x) > > [1] 41293 #probe sets > >> length(unique(x)) > > [1] 19944 #gene symbols > >> ind=grep("_x", names(x)) > >> summary(x[ind] %in% x[-ind]) > > Mode FALSE TRUE NA's > > logical 623 2469 0 > >> > > > > So for hgu133plus2 you would lose 623 out of 19944 genes - IMO if that > > changes your GSEA in an important way, it probably wasn't a robust result > > anyways. > > > > > > > > > > > > > >> > >> On Tue, Jul 30, 2013 at 9:00 AM, Levi Waldron < > lwaldron.research@gmail.com > >>> wrote: > >> > >>> Hi Feng, > >>> > >>> probe sets labelled with "_x" cross-hybridize to multiple genes: > >>> > >>> http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.jsp > >>> > >>> Genecards gives more detail for this probe set: > >>> > >>> > >>> > http://genecards.weizmann.ac.il/cgi-bin/geneannot/GA_search.pl?keywo rd_type=probe_set_id&array=HG-U133&target=genecards&keyword=200012_x_a t > >>> > >>> How to handle such a case depends on how interested you are in that > probe > >>> set; at the extremes you could ignore it, or follow up with PCR to > >>> establish which transcript you are observing. > >>> > >>> -Levi > >>> > >>> > >>> On Mon, Jul 29, 2013 at 6:06 PM, Feng Tian <fengtian@bu.edu> wrote: > >>> > >>>> Dear all, > >>>> > >>>> In the Affymetrix annotation file, I find that some probe set ID are > >>> mapped > >>>> to multiple genes separated by '///', such as 200012_x_at is mapped > >>>> to RPL21P16///RPL21P119///RPL21. How to handle this case? > >>>> > >>>> Thank you! > >>>> > >>>> Feng > >>>> > >>>> [[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 > >>>> > >>> > >>> > >>> > >>> -- > >>> Levi Waldron > >>> Post-doctoral fellow > >>> Department of Biostatistics, Harvard School of Public Health > >>> Department of Biostatistics and Computational Biology, Dana- Farber > Cancer > >>> Institute > >>> Building 1, room 412C > >>> 655 Huntington Avenue > >>> Boston, Massachusetts 02115 > >>> mobile: (617) 851-6849 > >>> fax: (617) 432-5619 > >>> http://www.hsph.harvard.edu/research/levi-waldron/ > >>> > >>> [[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]] > > > > _______________________________________________ > > 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 REPLY • link 11.3 years ago Levi Waldron ★ 1.1k

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