Introduction to dChip

DNA-Chip Analyzer (dChip) ( 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.

Download the dChip software (e.g. dchip2006.exe) and gene information files and store them into a local directory, and double-click the program icon to start dChip. This manual is written in a tutorial style. You may explore the functions that interest you by following the steps described in the manual. Paragraphs labeled as “[Analysis example]” may be skipped in the first reading. Please cite Li and Wong 2001a if dChip results are used in manuscripts, and cite Lin et al. 2004 if dChip SNP analysis functions are used.

Other academic microarray analysis software include: Cluster/TreeView, BioConductor, BRB ArrayTools, Cytoscape, GenePattern, GenMAPP, GoSurfer, GSEA, SAM, TM4.