Due to the need to protect personal information and the impracticality of exhaustive data collection, there is increasing need to deal with datasets with various levels of granularity, such as user-individual data and user-group data. In this study, we propose a new method for jointly analyzing multiple datasets with different granularity. The proposed method is a probabilistic model based on nonnegative matrix factorization, which is derived by introducing latent variables that indicate the high-resolution data underlying the low-resolution data. Experiments on purchase logs show that the proposed method has a better performance than the existing methods. Furthermore, by deriving an extension of the proposed method, we show that the proposed method is a new fundamental approach for analyzing datasets with different granularity.