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