[BioC] Clustering of 30,000+ genes

January Weiner january.weiner at gmail.com
Wed Sep 7 23:29:59 CEST 2011


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,



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