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Background  Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data. Not removing duplicates could lead false positive finding, misleading clustering pattern or model over-fitting issue, etc in the subsequent data analysis.    Results  We developed a Bioconductor package Dupchecker that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data. A real data example was demonstrated to show the usage and output of the package.    Conclusions  Researchers may not pay enough attention to checking and removing duplicated samples, and then data contamination could make the results or conclusions from meta-analysis questionable. We suggest applying DupChecker to examine all gene expression data sets before any data analysis step.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2105-15-323) contains supplementary material, which is available to authorized users.

DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis