A gene assaying method includes the steps of: acquiring two or more data which should be compared and represents expression levels of a plurality of target genes; converting the expression levels represented by the acquired two or more data into ratios based on the expression level of one of the two or more data; extracting a minimum ratio and a maximum ratio of each target gene; and classifying the plurality of target genes using as a classification border at least one of a first ratio with the peak in a frequency distribution of the minimum ratios and a second ratio with the peak in a frequency distribution of reciprocals of the maximum ratios.