Genomic FISHing: data analysis for chromosomal imbalances using DNA arrays

Microarrays for genomic analysis pose a rather serious challenge for statistical inference on the quality of data. With the ability to attach large genomic fragments on the array substrate, it is now possible to search for chromosomal imbalances related to various diseases at a significantly improved resolution. The challenge lies in understanding the experimental characteristics and modeling the erroneous noise to analyze and interpret the data. This paper presents a method of analysis that addresses the issues related to background noise, dye non-linearities, normalization, and replicate analysis. Data from three different cases is presented.