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Unequal group variances in microarray data analyses
Örebro University, Swedish Business School at Örebro University.
2008 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 24, no 9, p. 1168-1174Article in journal (Refereed) Published
Abstract [en]

Motivation: In searching for differentially expressed (DE) genes in microarray data, we often observe a fraction of the genes to have unequal variability between groups. This is not an issue in large samples, where a valid test exists that uses individual variances separately. The problem arises in the small-sample setting, where the approximately valid Welch test lacks sensitivity, while the more sensitive moderated t-test assumes equal variance. Methods: We introduce a moderated Welch test (MWT) that allows unequal variance between groups. It is based on (i) weighting of pooled and unpooled standard errors and (ii) improved estimation of the gene-level variance that exploits the information from across the genes. Results: When a non-trivial proportion of genes has unequal variability, false discovery rate (FDR) estimates based on the standard t and moderated t-tests are often too optimistic, while the standard Welch test has low sensitivity. The MWT is shown to (i) perform better than the standard t, the standard Welch and the moderated t-tests when the variances are unequal between groups and (ii) perform similarly to the moderated t, and better than the standard t and Welch tests when the group variances are equal. These results mean that MWT is more reliable than other existing tests over wider range of data conditions. Availability: R package to perform MWT is available at http://www.meb.ki.se/similar to yudpaw Contact: yudi.pawitan@ki.se Supplementary information: Supplementary data are available at Bioinformatics online.

Place, publisher, year, edition, pages
2008. Vol. 24, no 9, p. 1168-1174
National Category
Probability Theory and Statistics
Research subject
Statistics
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URN: urn:nbn:se:oru:diva-13618DOI: 10.1093/bioinformatics/btn100ISI: 000255313900007OAI: oai:DiVA.org:oru-13618DiVA, id: diva2:389244
Available from: 2011-01-19 Created: 2011-01-12 Last updated: 2017-12-11Bibliographically approved

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Demissie, Meaza

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CiteExportLink to record
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Citation style
  • apa
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  • de-DE
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