1. A manufacture data analysis method running on a processor, comprising: acquiring and storing manufacture data comprising a plurality of values of explanatory variables of a plurality of manufacture processes and an objective variable indicating quality of a product manufactured by a plurality of the manufacture processes; separating a plurality of the stored manufacture data into a set of manufacture data in which an explanatory variable value is missing and a set of manufacture data in which an explanatory variable value is not missing; separating the set of manufacture data in which the explanatory variable value is not missing, into a first set and a second set, calculating value of influence data based on a difference between a mean value of an objective variable of the first set and a mean value of an objective variable of the second set, and separating the first set and the second set so that the value of the influence data becomes a maximum; calculating a deficiency influence rate indicating a probability of having different analysis results between when the analysis includes the sets of manufacture data in which the explanatory variable is missing and when the analysis does not include the manufacture data in which the explanatory variable is missing but includes the first and second sets of the manufacture data; evaluating whether or not a missing value of the explanatory variable influences an analysis result based on the value of the influence data and the deficiency influence rate; and generating the analysis result for later use.