[BioC] Clustering in R

wmak at brandeis.edu wmak at brandeis.edu
Wed Jun 16 22:26:02 CEST 2004

Dear list members,

I'm an undergrad and I work in a lab at Brandeis.  I am trying to cluster
around 14,000 genes across 6 microarray experiments.  Two of these experiments
are replicates.  I have decided to use R since it seems to be the most
complete and flexible software package for normalization and clustering of
microarray data.

The problem is that I am new to clustering and to R.  Just to mention of a few
of the problems I'm having: the dendrogram that is drawn by R from the agnes
object is far too dense to see any of the gene names; kmeans won't work,
returning an error saying that my data has NAs in it (there weren't any
missing values in the original table though); I'd like to be able to see a
heatmap or a cumulative plot of expression profiles for genes that are
clustered together or are on the same branch of the dendrogram.

I know that these questions are probably very simple, but I can't seem to find
the answer to them online or in the documentation.  If anyone can answer these
questions or direct me toward resources that deal with clustering in R or
BioConductor, a basic tutorial that takes a practical approach to it, I would
really appreciate it.  Any other reading material that isn't too heavy on
statistics that deals with clustering for that matter, would be very helpful.

Thank you in advance,

Wayne Mak

More information about the Bioconductor mailing list