A software package for cDNA microarray data normalization and assessing confidence intervals

DNA microarray data are affected by variations from a number of sources. Before these data can be used to infer biological information, the extent of these variations must be assessed. Here we describe an open source software package, lcDNA, that provides tools for filtering, normalizing, and assessing the statistical significance of cDNA microarray data. The program employs a hierarchical Bayesian model and Markov Chain Monte Carlo simulation to estimate gene-specific confidence intervals for each gene in a cDNA microarray data set. This program is designed to perform these primary analytical operations on data from two-channel spotted, or in situ synthesized, DNA microarrays.