Table of Contents
DNA-Chip Analyzer (dChip) is a software package implementing model-based expression analysis of oligonucleotide arrays (Li and Wong 2001a) and several high-level analysis procedures. The model-based approach allows probe-level analysis on multiple arrays. By pooling information across multiple arrays, it is possible to assess standard errors for the expression indexes. This approach also allows automatic probe selection in the analysis stage to reduce errors due to cross-hybridizing probes and image contamination. High-level analysis in dChip includes comparative analysis and hierarchical clustering. Also see the comparison with Affy MAS software.
Download software at dChip website: http://www.dchip.org/
This is an ongoing effort to move dChip manual and useful discussions at dChip Yahoo group to this WikiBook. Feel free to help out or share your own dChip experiences here, e.g. by adding data analysis examples or links to your paper using dChip.