A method for analyzing a wafer map using a wafer map analyzer includes generating first wafer maps each displaying characteristics of a first wafer for a corresponding channel of a plurality of channels. The first wafer maps are auto-encoded together to extract a first feature. The method also includes determining whether the first feature is a valid pattern, classifying the type of the first feature based on unsupervised learning when the first feature is a valid pattern and extracting a representative image of features classified into the same type as the first feature.