Dear group, apologies this question is not directed to any bioconductor package, but a simple bioinformatics question. I have gene expression data cDNA array. The design is: total 6 samples (3 treated, 3 untreated) with time points. Time 1: Sample1-treated/Sample1-untreated Time 2: Sample 2- treated / Sample 2-untreated Time 3 : Sample 3 - treated / Sample - 3 untreated Now I have fold-changes for Time1, Time2 and Time3. Is it possible to do a clustering here by creating a matrix: Genes Time-1 Time-2 Time-3 G1 G2 .. Is doing a simple Hierarchical clustering between all time points a meaningful approach because the fold changes are specific to a particular time point. (reference samples is not universal but specific to a timepoint). Could anyone kindly educate me here. Apologies again if this question is a misfit. Thanks Srini ________________________________________________________________ ____________________ Never miss a thing. Make Yahoo your home page.