Bootstrap method for the estimation of measurement uncertainty in spotted dual-color DNA microarrays

DNA microarrays permit the measurement of gene expression across the entire genome of an organism, but the quality of the thousands of measurements is highly variable. For spotted dual-color microarrays the situation is complicated by the use of ratio measurements. Studies have shown that measurement errors can be described by multiplicative and additive terms, with the latter dominating for low-intensity measurements. In this work, a measurement-error model is presented that partitions the variance into general experimental sources and sources associated with the calculation of the ratio from noisy pixel data. The former is described by a proportional (multiplicative) structure, while the latter is estimated using a statistical bootstrap method. The model is validated using simulations and three experimental data sets. Monte-Carlo fits of the model to data from duplicate experiments are excellent, but suggest that the bootstrap estimates, while proportionately correct, may be underestimated. The bootstrap standard error estimates are particularly useful in determining the reliability of individual microarray spots without the need for replicate spotting. This information can be used in screening or weighting the measurements.