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Benjamin Otto wrote: > Dear community, > > > > When I look at Dchip cluster the expression value range is most of the time > between -2 and 2. That's because the standard options lead to a z-score > standardization of values. > You need to ask the author of dChip these questions, as only they would really know the answer. It is not open source. I believe they run their own mailing list www.dchip.org) best wishes Robert > > > 1) Does anybody know whether this procedure is performed before or > after clustering? > > 2) The procedure seems to return nice visual contrasts for clusters of > already determined target genes. However it distorts the ratio/relationship > between the single genes AND samples > > a. visually if applied after clustering and > > b. in addition leads to different clusters if applied before > clustering. > > So is there some good reason (beyond contrasting) to use the z-score BEFORE > clustering? > > > > > > Regards > > > > Benjamin > > > > > > > > > > > > -- > Benjamin Otto > Universitaetsklinikum Eppendorf Hamburg > Institut fuer Klinische Chemie > Martinistrasse 52 > 20246 Hamburg > > > > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Here is a jpg-image demonstrating the effect of the z-scoring I mean. The only difference in the three displayed cases is the application of the z-score and when it is applied. The center image corresponds to point 2a in my post and the right image corresponds to 2b. p.S.: I hope the image passes the admin curration, I couldn't get it smaller than 160kb. Regards benjamin -----Urspr?ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Benjamin Otto Gesendet: 03 November 2006 14:08 An: 'BioClist' Betreff: [BioC] contrasting cluster images Dear community, When I look at Dchip cluster the expression value range is most of the time between -2 and 2. That's because the standard options lead to a z-score standardization of values. 1) Does anybody know whether this procedure is performed before or after clustering? 2) The procedure seems to return nice visual contrasts for clusters of already determined target genes. However it distorts the ratio/relationship between the single genes AND samples a. visually if applied after clustering and b. in addition leads to different clusters if applied before clustering. So is there some good reason (beyond contrasting) to use the z-score BEFORE clustering? Regards Benjamin -- Benjamin Otto Universitaetsklinikum Eppendorf Hamburg Institut fuer Klinische Chemie Martinistrasse 52 20246 Hamburg [[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