Multidimensional data sets often include categorical information. When most dimensions have categorical information, clustering the data set as a whole can reveal interesting patterns in the data set. However, the categorical information is often more useful as a way to partition the data set: gene expression data for healthy versus diseased samples or stock performance for common, preferred, or convertible shares. We present novel ways to utilize categorical information in exploratory data analysis by enhancing the rank-by-feature framework. First, we present ranking criteria for categorical variables and ways to improve the score overview. Second, we present a novel way to utilize the categorical information together with clustering algorithms. Users can partition the data set according to categorical information vertically or horizontally, and the clustering result for each partition can serve as new categorical information. We report the results of a longitudinal case study with a biomedical research team, including insights gained and potential future work.

MOTIVATION: Human clinical projects typically require a priori statistical power analyses. Towards this end, we sought to build a flexible and interactive power analysis tool for microarray studies integrated into our public domain HCE 3.5 software package. We then sought to determine if probe set algorithms or organism type strongly influenced power analysis results. RESULTS: The HCE 3.5 power analysis tool was designed to import any pre-existing Affymetrix microarray project, and interactively test the effects of user-defined definitions of alpha (significance), beta (1-power), sample size and effect size. The tool generates a filter for all probe sets or more focused ontology-based subsets, with or without noise filters that can be used to limit analyses of a future project to appropriately powered probe sets. We studied projects from three organisms (Arabidopsis, rat, human), and three probe set algorithms (MAS5.0, RMA, dChip PM/MM). We found large differences in power results based on probe set algorithm selection and noise filters. RMA provided high sensitivity for low numbers of arrays, but this came at a cost of high false positive results (24% false positive in the human project studied). Our data suggest that a priori power calculations are important for both experimental design in hypothesis testing and hypothesis generation, as well as for the selection of optimized data analysis parameters. AVAILABILITY: The Hierarchical Clustering Explorer 3.5 with the interactive power analysis functions is available at www.cs.umd.edu/hcil/hce or www.cnmcresearch.org/bioinformatics. CONTACT: [email protected]