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TECHNICAL ADVANCE: EVE (external variance estimation) increases statistical power for detecting differentially expressed genes
Author(s) -
Wille Anja,
Gruissem Wilhelm,
Bühlmann Peter,
Hennig Lars
Publication year - 2007
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2007.03227.x
Subject(s) - variance (accounting) , biology , gene , microarray analysis techniques , microarray , statistical hypothesis testing , computational biology , genetics , data mining , computer science , gene expression , statistics , mathematics , accounting , business
Summary Accurately identifying differentially expressed genes from microarray data is not a trivial task, partly because of poor variance estimates of gene expression signals. Here, after analyzing 380 replicated microarray experiments, we found that probesets have typical, distinct variances that can be estimated based on a large number of microarray experiments. These probeset‐specific variances depend at least in part on the function of the probed gene: genes for ribosomal or structural proteins often have a small variance, while genes implicated in stress responses often have large variances. We used these variance estimates to develop a statistical test for differentially expressed genes called EVE (external variance estimation). The EVE algorithm performs better than the t ‐test and LIMMA on some real‐world data, where external information from appropriate databases is available. Thus, EVE helps to maximize the information gained from a typical microarray experiment. Nonetheless, only a large number of replicates will guarantee to identify nearly all truly differentially expressed genes. However, our simulation studies suggest that even limited numbers of replicates will usually result in good coverage of strongly differentially expressed genes.