DNA-Chip Analyzer (dChip) (www.dchip.org) is a Windows software package for probe-level (e.g. Affymetrix platform) and high-level analysis of gene expression microarrays and SNP microarrays (Li and Wong 2001a, Lin et al. 2004). Gene expression or SNP data from various microarray platforms can also be analyzed by importing as external dataset. At the probe level, dChip can display and normalize the CEL files, and the model-based approach allows pooling information across multiple arrays and automatic probe selection to handle cross-hybridization and image contamination. High-level analysis in dChip includes comparing samples, hierarchical clustering, view expression and SNP data along chromosome, LOH and copy number analysis of SNP arrays, and linkage analysis. In these functions the gene information and sample information are correlated with the analysis results.