[BioC] Clustering of 30,000+ genes

[Naomi Altman]

Try WGCNA which is available from CRAN.

--Naomi

At 05:29 PM 9/7/2011, January Weiner wrote:
>Hello,
>
>I'm struggling with co-expression analysis, and for that I would like
>to try to cluster all the genes I have in my microarray set, including
>those which are not differentially expressed between the study groups.
>I am using CoXpress at the moment and will try my luck with GSCA as
>well, but both packages seem to have been layed out for 3000 rather
>than 30000 genes.
>
>How do you do that in R? I get errors about R not being able to
>allocate enough memory. Clearly, the amount of memory required to
>calculate all correlations the simple way might be a bit on the large
>side, but I can think of one or two tricks to get this done; I wonder
>whether it has been implemented already.
>
>Other than that -- how should I reasonably limit the number of genes
>to study? i don't want to bias the outcome of the analysis by
>selecting only genes that are DE, actually -- I would be very
>interested in genes that  show differential co-expression, but no
>differences in expression.
>
>Kind regards,
>
>j.
>
>--
>
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