Generalized singular values (GSVs) play an essential role in the comparative analysis. In the real world data for comparative analysis, both data matrices are usually numerically low-rank. This paper proposes a randomized algorithm to first approximately extract bases and then calculate GSVs efficiently. The accuracy of both basis extration and comparative analysis quantities, angular distances, generalized fractions of the eigenexpression, and generalized normalized Shannon entropy, are rigursly analyzed. The proposed algorithm is applied to both synthetic data sets and the genome-scale expression data sets. Comparing to other GSVs algorithms, the proposed algorithm achieves the fastest runtime while preserving sufficient accuracy in comparative analysis.

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