DNA microarray image processing has vast potential in the measurement of mass gene expression. A common approach to processing microarrays consists of spot identification, spot segmentation, and information extraction. We are concerned with spot identification. We aim to tackle the problem of identifying spots in rotated and skewed arrays via an automated process. The method proposed is composed of three steps, namely, array orientation calculation based on the Hough transform, affine calculation and correction, and gridding. The method is able to correctly identify spots in a microarray that has been rotated or skewed at an angle between 0 and ±30 deg and corrupted by various types of noise such as high-intensity streaks, Gaussian noise, and salt-and-pepper noise.