gene level on exon chip?
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Paul Hammer ▴ 220
@paul-hammer-2635
Last seen 9.6 years ago
hi members, is there any function or easy way to get the gene level of a human exon affymetrix chip? currently i calculate the average of all exonic probeset intensities for genes of interest individually. other question what i have is there any easy way to remove poor performing probesets via DABG (detection above background score)? many thanks and best regards paul > sessionInfo() R version 2.6.2 (2008-02-08) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] exonmap_1.4.3 plier_1.8.0 RMySQL_0.6-0 [4] DBI_0.2-4 RColorBrewer_1.0-2 simpleaffy_2.14.05 [7] gcrma_2.10.0 matchprobes_1.10.0 genefilter_1.16.0 [10] survival_2.34 affy_1.16.0 preprocessCore_1.0.0 [13] affyio_1.6.1 Biobase_1.16.3 loaded via a namespace (and not attached): [1] annotate_1.16.1 AnnotationDbi_1.0.6 rcompgen_0.1-17 [4] RSQLite_0.6-8
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cstrato ★ 3.9k
@cstrato-908
Last seen 5.5 years ago
Austria
Dear Paul For example, my package "xps" (available from BioC 2.2) is able to calculate normalized expression levels of exon arrays both at the gene level and at the probeset level. In addition, it can compute DABG calls also on the gene level and probeset level. You are even able to compute MAS5 calls for the exon arrays and compare the results to the DABG calls. I hope this info is helpful. Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._ Paul Hammer wrote: > hi members, > > is there any function or easy way to get the gene level of a human exon > affymetrix chip? currently i calculate the average of all exonic > probeset intensities for genes of interest individually. > > other question what i have is there any easy way to remove poor > performing probesets via DABG (detection above background score)? > > many thanks and best regards > paul > > > > sessionInfo() > R version 2.6.2 (2008-02-08) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] exonmap_1.4.3 plier_1.8.0 RMySQL_0.6-0 > [4] DBI_0.2-4 RColorBrewer_1.0-2 simpleaffy_2.14.05 > [7] gcrma_2.10.0 matchprobes_1.10.0 genefilter_1.16.0 > [10] survival_2.34 affy_1.16.0 preprocessCore_1.0.0 > [13] affyio_1.6.1 Biobase_1.16.3 > > loaded via a namespace (and not attached): > [1] annotate_1.16.1 AnnotationDbi_1.0.6 rcompgen_0.1-17 > [4] RSQLite_0.6-8 > > _______________________________________________ > 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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Hi Paul. Another option is the 'aroma.affymetrix' package: http://groups.google.com/group/aroma-affymetrix Specifically, have a look at: http://groups.google.com/group/aroma-affymetrix/web/human-exon-array- analysis ... there is a section called "Summarization" which talks about getting gene-level (or probeset-level) summaries. Taking averages of probeset summaries should perform very badly. Cheers, Mark On 16/04/2008, at 7:38 AM, cstrato wrote: > Dear Paul > > For example, my package "xps" (available from BioC 2.2) is able to > calculate normalized expression levels of exon arrays both at the gene > level and at the probeset level. In addition, it can compute DABG > calls > also on the gene level and probeset level. You are even able to > compute > MAS5 calls for the exon arrays and compare the results to the DABG > calls. > > I hope this info is helpful. > Best regards > Christian > _._._._._._._._._._._._._._._._ > C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a > V.i.e.n.n.a A.u.s.t.r.i.a > e.m.a.i.l: cstrato at aon.at > _._._._._._._._._._._._._._._._ > > > Paul Hammer wrote: >> hi members, >> >> is there any function or easy way to get the gene level of a human >> exon >> affymetrix chip? currently i calculate the average of all exonic >> probeset intensities for genes of interest individually. >> >> other question what i have is there any easy way to remove poor >> performing probesets via DABG (detection above background score)? >> >> many thanks and best regards >> paul >> >> >>> sessionInfo() >> R version 2.6.2 (2008-02-08) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_U >> S.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U >> S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT >> F-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils >> datasets >> [8] methods base >> >> other attached packages: >> [1] exonmap_1.4.3 plier_1.8.0 RMySQL_0.6-0 >> [4] DBI_0.2-4 RColorBrewer_1.0-2 simpleaffy_2.14.05 >> [7] gcrma_2.10.0 matchprobes_1.10.0 genefilter_1.16.0 >> [10] survival_2.34 affy_1.16.0 preprocessCore_1.0.0 >> [13] affyio_1.6.1 Biobase_1.16.3 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.16.1 AnnotationDbi_1.0.6 rcompgen_0.1-17 >> [4] RSQLite_0.6-8 >> >> _______________________________________________ >> 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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