Obtain the dChip software 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. It is best to explore the functionalities of dChip by following the steps described here sequentially. Paragraphs labeled as “[Analysis example]” may be skipped in first reading. Please cite Li and Wong 2001a if dChip results are used in manuscripts.

dChip is a single executable program running on Windows 2000, under which it is being developed. Presumably it can also run properly on Windows NT/XP, but some functions such as clustering picture zooming and image saving do not work properly on Windows 95/98. The computer memory should be as large as the number of chips (e.g. if there are 100 chips to analyze together, we need > 100M memory), since dChip reads in all CEL data of a group of arrays into the memory. dChip is written in Visual C++ and uses Windows-specific functions for graphic tasks. Victoria Perreau has run dChip on an iBook, using the Connectix Virtual PC Windows 2000 software which costs about $225. When running on the iBook (466 MHz, 320 RAM) it takes about 7 times longer to do the analysis than a PC (1000Mhz Pentium III , 256RAM), i.e. 6 CEL files are normalized in 8 minutes instead of 1.