Hi Paul, This article may also be of interest: "Exon arrays provide accurate assessments of gene expression" (http://genomebiology.com/2007/8/5/R82). Though it doesn't look like they have an R implementation. Regards, -Steve ---------------------------------------------------------------- Stephen Piccolo PhD Student Department of Biomedical Informatics, University of Utah Salt Lake City, UT 84112-5750 My Informatics Blog: http://biomedicalinformatics.wordpress.com ----------------------------------------------------------------- -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of cstrato Sent: Friday, April 18, 2008 4:57 AM To: Paul Hammer Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] [Fwd: Re: gene level on exon chip?] Dear Paul Please let me comment on Michal's warning: Even the Affymetrix people claim that you can use the exon arrays to compute gene expression levels, however, I agree with Michal that you must be careful. Affymetrix has divided the probesets into (meta)core, extended and full. If you select only (meta)core (which you can do with xps) then my experience shows that you are on the save side. Since you want to compare your results with gene chips, Affymetrix provides "BestMatch" files for this purpose. The following paper of Robinson & Speed, who compare HuExon to HuGene and HGU133plus2 arrays may also be of interest to you: http://www.biomedcentral.com/1471-2105/8/449 Best regards Christian Paul Hammer wrote: > > > ---------------------------------------------------------------------- -- > > Subject: > Re: [BioC] gene level on exon chip? > From: > Paul Hammer <paul.hammer at="" p-t-p.de=""> > Date: > Thu, 17 Apr 2008 16:56:37 +0200 > To: > Michal Okoniewski <michal.okoniewski at="" fgcz.ethz.ch=""> > > To: > Michal Okoniewski <michal.okoniewski at="" fgcz.ethz.ch=""> > > > Michal Okoniewski schrieb: >> Just a small warning Paul... There is no such thing as "gene level" >> expression, especially with exon chips. >> There are various affinities, various amount of intronic and exonic >> probes within a gene and possible splicing of course. >> You can run gene level summarization with Christian's tool or with >> Brainarray CDF, but think of the >> interpretation - if it exists. Alternatively/complementarily I would >> eg. plot all your genes of interest in exonmap. >> >> Best, >> Michal >> >> 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 .U TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UT F- 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ ID ENTIFICATION=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 >>> >>> >> > first thanks for help... > > @ Christian and Mark: i have installed both packages just now. lets > see which is my favorite :) > > @ michal: you are absolutely right. i know only to well how hard it is > to interpret gene levels on exon chips. but i try to compare results > from exon chips with gene chips. by the way how are you calculating > the gene level within the function splicing.index()? > > cheers > paul > > > > ---------------------------------------------------------------------- -- > > _______________________________________________ > 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