1. A microarray analysis method in which a microarray obtained by arranging probes on a substrate surface having an irregular shape is irradiated with excitation light and fluorescence amounts of the probes excited by the excitation light are obtained as numerical data, the microarray analysis method comprising: immobilizing probes onto a substrate surface having an irregular shape to obtain a microarray, wherein the probes are selected from the group consisting of DNA, RNA, proteins, tissues, and low-molecular compounds; a step (a) for measuring the fluorescence amounts of the probes to acquire fluorescence image data; a step (b) for receiving reflected light and/or scattered light from the substrate surface to acquire the irregular shape of the substrate surface of the microarray as alignment image data based on light receiving intensities of the light; a step (c) for determining positions of the probes on the fluorescence image data based on the alignment image data, wherein the step (c) comprises: a step (c1) for detecting equal to or more than three reference points A of the microarray based on a difference in the light receiving intensities on the alignment image data, wherein step (c1) comprises: a step of calculating a contour reference point a as points on a contour of the substrate on each of at least eight predetermined observation regions; a step of pairing at least two predetermined observation regions that are not overlapped as sets to obtain approximate straight lines with respect to a plurality of contour reference points A for the respective sets; and a step of calculating intersecting points of the approximate straight lines obtained for the respective sets to set the intersecting points as the reference points A; and a step (c2) for correcting shear deformation strain of the fluorescence image data based on the detected reference points A and to provide a corrected fluorescence image.