Estimation of Correlation between Various Types of Pixel Intensities in a Single Spot

In cDNA microarray experiments, the measurement of interest is signal intensity ratio of spots. Each spot have four types of pixel intensities namely red foreground, green foreground, red background and green background. The uncertainty associated with the intensity ratio of a spot depends on the correlations between intensities of these pixels. In this article, we propose a method to estimate correlations between various types of pixel intensities within a spot using a modified form of Moran’s I spatial autocorrelation. We estimate these correlations for eight selected spots from image files downloaded from the Gene Expression Omnibus (GEO) database. These estimated correlations are used for finding the uncertainty associated with each of the selected eight spots using the theory of error propagation. We observed that the estimated uncertainty associated with intensity ratio of a spot is less if we consider the correlation between various pixel intensities compared to assuming zero correlation.