Can we trust biomarkers? visualization and quantification of outlier probes in high density oligonucleotide microarrays

One of the top priorities in translating genomics to disease diagnosis and treatment is the reliability and reproducibility of oligonucleotide microarrays. Previous work such as dChip (Li and Wong, 2001) and caCORRECT (Stokes et al., 2007) have tried to detect outlier probes and remove artifacts. This paper presents a more advanced method that quantifies and visualizes the direct impact of outlier probes on genes of interest (i.e. biomarkers). Thousands of papers on microarray have been published, and many of these papers have claimed to discover new biomarkers. However, many biomarkers cannot be reproduced. Using our research result, the wide community of microarray users can rescreen hundreds of oligo microarray data, and overlay previous published biomarkers so to get rid of noisy ones. The methods are being incorporated into the next version of caCORRECT, which is available at http://www.caCORRECT.bme.gatech.edu.