Scotty is a tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.
The HCE (Hierarchical Clustering Explorer) power analysis tool was designed to import any pre-existing microarray project, and interactively test the effects of user-defined definitions of α (significance), β (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 exquisite 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 suggests that a priori power calculations are important for both experimental design in hypothesis testing, and hypothesis generation, as well as for selection of optimized data analysis parameters.
POLY is a computer program for polygenic analysis and power analysis of human quantitative traits. It is convenient to use POLY to analyze multiple models / traits in large pedigrees