Robust microarray analysis

A successful sample preparation ensures robust microarray analysis, which requires high quality surfaces for the reaction between target and probe. Of the many different types of... 

Protein microarrays have many potential applications in high-throughput analysis of protein function. However, simple, reproducible, and robust methods for array fabrication are required. Here we discuss the background to different routes to array fabrication and describe in detail one approach in which the purification and immobilization procedures are combined into a single step, dramatically simplifying the array fabrication process. We illustrate this approach by reference to the creation of an array of p53 variants, and discuss methods for assay and data analysis on such arrays. 

Microarray data may require transformation to stabilize the variance by applying a global logarithmic transformation prior to normalization and further analysis. This may unpredictably skew the measurement, making further analysis difficult and unreliable (39). As many of the techniques used for the analysis of microarray data are not robust to the equal variance assumption, a family of variance stabilizing transformation (VST) methods for microarray data have been proposed (4CM14). 

Several different approaches to microarray construction have been developed, including oligonucleotide- or DNA-based arrays on glass slides or nylon membranes (10). Here, we describe a robust CGH protocol based on the use of a PCR-generated microarray (6). Detailed descriptions of genomic DNA template preparation, labeling, microarray hybridization, and data analysis are provided. 

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