Is there another way to analyze ChIP-chip data?
Yes, the following five sites have been developed to analyze ChIP-chip data. 1. M-peak: Nature. 2005 436(7052):876-80 2.TAMALPAIS Server: 2006 Genome Research 16:595. 3.ACME (in R language): Methods Enzymol. 2006;411:270-82. 4.ChIPOTle: Genome Biology 2005, 6:R97. For the Perl version, go to ChIPOTle Peak Finder 5.Model-based Analysis of 2-Color Arrays MA2C.