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Genome Biol. 2004;5(9):R70. Epub 2004 Aug 26.

Improving identification of differentially expressed genes in microarray studies using information from public databases.

Author information

  • 1Harvard-Partners Center for Genetics and Genomics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

Abstract

We demonstrate that the process of identifying differentially expressed genes in microarray studies with small sample sizes can be substantially improved by extracting information from a large number of datasets accumulated in public databases. The improvement comes from more reliable estimates of gene-specific variances based on other datasets. For a two-group comparison with two arrays in each group, for example, the result of our method was comparable to that of a t-test analysis with five samples in each group or to that of a regularized t-test analysis with three samples in each group. Our results are further improved by weighting the results of our approach with the regularized t-test results in a hybrid method.

PMID:
15345054
[PubMed - indexed for MEDLINE]
PMCID:
PMC522877
Free PMC Article

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