you might find the 'WCGNA' package to be useful for a starting point.  it
is also extensively published and IIRC, at least one of the authors is on
this list

Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>


On Tue, Feb 11, 2014 at 11:22 AM, Rafi [guest] <guest@bioconductor.org>wrote:

>
> Hi all,
>
> I am trying to find co-expressed genes in my affy data. I use hierarchical
> clustering with dynamic tree cut. I want to choose optimal clustering/cut
> parameters and I am new to cluster validation. I understand that there are
> many cluster indices that can be used for cluster validation.
>
> Since I am interested in co-expression only, can I simply use intraclass
> correlation (ICC) as a metric to choose optimal parameters? ie, choose the
> clustering parameters that gives the highest ICC in each cluster.
>
> Is ICC commonly used for choosing clustering parameters? Is it Ok? or Is
> there any other more commonly used metric?
>
> Thanks a lot in advance.
> Rafi
>
>
>
>  -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] GeneAnswers_2.4.0    RColorBrewer_1.0-5   Heatplus_2.8.0
> MASS_7.3-29          XML_3.98-1.1         RCurl_1.95-4.1
>  [7] bitops_1.0-6         igraph_0.6.6         plyr_1.8
> KEGG.db_2.10.1       GSEABase_1.24.0      rat2302.db_2.10.1
> [13] org.Rn.eg.db_2.10.1  annotate_1.40.0      GOstats_2.28.0
> graph_1.40.1         Category_2.28.0      Matrix_1.1-1.1
> [19] GO.db_2.10.1         RSQLite_0.11.4       DBI_0.2-7
>  AnnotationDbi_1.24.0 Biobase_2.22.0       BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>  [1] AnnotationForge_1.4.4 genefilter_1.44.0     grid_3.0.2
>  IRanges_1.20.6        lattice_0.20-24
>  [6] RBGL_1.38.0           splines_3.0.2         stats4_3.0.2
>  survival_2.37-4       tools_3.0.2
> [11] xtable_1.7-1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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