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Open Access Highly Accessed Research article

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

Joshua S Bloom, Zia Khan, Leonid Kruglyak, Mona Singh and Amy A Caudy*

BMC Genomics 2009, 10:221  doi:10.1186/1471-2164-10-221

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fisher's exact test for differential expression analysis

Ann Loraine   (2009-05-28 14:14)  UNC Charlotte email

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.

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