Acquisition of Accurate Gene Expression Information from Microarray Measurements

Gene expression profiling using microarray technology has become an important genetic tool in the study of complex diseases. However, this technology is prone to noise and the accuracy of its measurements is often in question. Here, we describe the technological and analytical advancements that we have made in microarrays to overcome this problem. We have extended the conventional dual-color spotted microarray technology to a novel three-color microarray platform, where the probes on printed arrays are labeled with a third dye for quality control (QC) in array fabrication. We have also developed a microarray image analysis package called Matarray, which achieves quantitative QC of data acquisition through the definition of a set of quality scores. With these advances, a better dissection of the sources of data variability and more efficient QC are achieved. In addition, our data QC approach has led to a new weighted statistical procedure for evaluating the significance of microarray findings that can more sensitively detect changes in gene expression. This resolves the missing value problem that has often plagued microarray data analysis. Finally and most importantly, we show that with our analytical and technical advancements, where a comprehensive and efficient QC procedure is in place, accurate gene expression measurements comparable in quality to those by quantitative reverse transcription–polymerase chain reaction (RT-PCR) can be achieved with microarrays fabricated in academic laboratories.