[BioC] contrasting cluster images

[Robert Gentleman]

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