The remarkably increasing rate at which genomes are being sequenced has opened a new area of genome research, functional genomics, which is concerned with assigning biological function to DNA sequences. The novel biotechnologies such as cDNA microarrays and oligonucleotide chips are increasingly used to exploit DNA sequence data and yield information on the gene expression levels for entire genomes.

Many statisticians have developed some statistical methods for designing and analyzing microarray gene expression data. However, most of the commercial softwares do not fully cover these statistical methods but only emphasize the visualization tools and user-friendly operating tools. It is still not easy for the biologists to use the appropriate statistical software and interpret the results.. Thus, we developed an integrated statistical software system for analyzing DNA chip data, ISSAC. It is as user-friendly as the other commercial softwares and implements many recently proposed statistical methods.