[BioC] cross validation / bootstrap after classification

[Kevin Coombes]

Hi,

I have a package (ClassDiscovery) at
	http://bioinformatics.mdanderson.org/Software/OOMPA
that includes classes for
	PerturbationClusterTest
and
	BootstrapClusterTest.

Richard Simon's book (Design and Analysis of DNA Microarray Experiments) 
includes a section on assesing the validity of clusters.

Of course, clusters arising from a supervised selection of genes aren't 
meaningful anyway....

  -- Kevin

--On Friday, November 04, 2005 1:40 PM +0100 Heike Pospisil 
<pospisil at zbh.uni-hamburg.de> wrote:

> Hello Bioconducters,
>
> I used t-test and/or SAM to find significant genes describing the
> differences in  hgu133plus2-chips of two different phenotypical classes.
> The resulting heatmaps  show a promising clustering.
>
> Now, I would like to confirm these clusters and to estimate the
> robustness of  this clustering by cross-validation and/or
> bootstrapping(*). For that, I have  two questions:
>
> 1) Does there exists an appropriate package and/or source to perfom
> cross-validation and/or bootstrapping?
>
> 2) Which is the right measure to rate the goodness of such a clustering?
> By now,  I looked over the cluster plots(**) and decided if it was good
> or a bad clustering.
>
> Thanks in advance for any suggestion.
> Best wishes,
> Heike
>
> *  with varying chip - subsets
> ** heatmap(exprs(sub),Colv=as.dendrogram(hclust(dist(t(exprs(sub)),
> method="euclidean"),method="complete")))
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor