Hi Tim, Thanks for your recommendation. I have looked at both packages but I am not sure whether that is what what I need. I would like to cluster or visualize (graphically if possible) the array expression values (and or CN values of CCLE) of 5 cancer cell lines, (the cell lines are in columns, the genes are in row). Ideally we can find out the pattern and display the hierarchical cluster as well. Can you explain a little details about these when possible? Thanks! Ran -----Original Message----- From: Tim Triche, Jr. [mailto:tim.triche@gmail.com] Sent: Sunday, February 09, 2014 12:52 AM To: Chen Runtian Cc: Bioconductor mailing list Subject: Re: [BioC] cluster or pattern analysis of expression and CN data of cell lines epigenomix or pint --t > On Feb 8, 2014, at 1:48 AM, Chen Runtian <chenruntian at="" hdbiosciences.com=""> wrote: > > I am analyzing (or reanalyzing) the gene expression data and copy number (CN) - (i.e from CCLE) of 5 cell cancer cell lines, and hope to find out the pattern or cluster for genes in those cell lines. Can someone suggest me a tool or tools to analyze and visualize the pattern or cluster? > > Thank you! > > Ran > > > The information transmitted is intended only for the p...{{dropped:16}}