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Archived Comments for: Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

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  1. fisher's exact test for differential expression analysis

    Ann Loraine, UNC Charlotte

    28 May 2009

    I'm curious about the authors' use of Fisher's exact test of contingency tables for the short-reads differential expression testing. It's an easy test to perform and it would be great if it's appropriate to use in this setting. But I think the contingency tables, if I understand the approach, will have vastly different numbers in the cells of the table. How does the test perform under these conditions? I would welcome some additional discussion of this issue.

    Competing interests

    No competing interests.