Document Detail


Microarray test results should not be compensated for multiplicity of gene contents.
MedLine Citation:
PMID:  22784577     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
BACKGROUND: Microarray technology has enabled the measurement of comprehensive transcriptomic information. However, each data entry may reflect trivial individual differences among samples and also contain technical noise. Therefore, the certainty of each observed difference should be confirmed at earlier steps of the analyses, and statistical tests are frequently used for this purpose. Since microarrays analyze a huge number of genes simultaneously, concerns of multiplicity, i.e. the family wise error rate (FWER) and false discovery rate (FDR), have been raised in testing the data. To deal with these concerns, several compensation methodologies have been proposed, making the tests very conservative to the extent that arbitrary tuning of the threshold has been introduced to relax the conditions. Unexpectedly, however, the appropriateness of the test methodologies, the concerns of multiplicity, and the compensation methodologies have not been sufficiently confirmed.
RESULTS: The appropriateness was checked by means of coincidence between the methodologies' premises and the statistical characteristics of data found in two typical microarray platforms. As expected, normality was observed in within-group data differences, supporting application of t-test and F-test statistics. However, genes displayed their own tendencies in the magnitude of variations, and the distributions of p-values were rather complex. These characteristics are inconsistent with premises underlying the compensation methodologies, which assume that most of the null hypotheses are true. The evidence also raised concerns about multiplicity. In transcriptomic studies, FWER should not be critical, as analyses at higher levels would not be influenced by a few false positives. Additionally, the concerns for FDR are not suitable for the sharp null hypotheses on expression levels.
CONCLUSIONS: Therefore, although compensation methods have been recommended to deal with the problem of multiplicity, the compensations are actually inappropriate for transcriptome analyses. Compensations are not only unnecessary, but will increase the occurrence of false negative errors, and arbitrary adjustment of the threshold damages the objectivity of the tests. Rather, the results of parametric tests should be evaluated directly.
Authors:
Tomokazu Konishi
Related Documents :
22674707 - A survey of the practice and management of radiotherapy linear accelerator quality cont...
22585237 - Molecular diagnosis of old world leishmaniasis: real-time pcr based on tryparedoxin per...
22357557 - Concept and validation of a fully automated photocatalytic test setup.
22796097 - Prediction of skin sensitization potency of chemicals by human cell line activation tes...
18407027 - Effect of fluoride varnish on enamel demineralization around brackets: an in-vivo study.
18317367 - Validity of the caler and omni-bike ratings of perceived exertion.
Publication Detail:
Type:  Journal Article     Date:  2011-12-14
Journal Detail:
Title:  BMC systems biology     Volume:  5 Suppl 2     ISSN:  1752-0509     ISO Abbreviation:  BMC Syst Biol     Publication Date:  2011 Dec 
Date Detail:
Created Date:  2012-07-12     Completed Date:  2012-11-16     Revised Date:  2013-07-12    
Medline Journal Info:
Nlm Unique ID:  101301827     Medline TA:  BMC Syst Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  S6     Citation Subset:  IM    
Affiliation:
Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan. konishi@akita-pu.ac.jp
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Computer Simulation
Databases, Genetic
Gene Expression Profiling / methods*
Genes*
Humans
Microarray Analysis / methods*
Models, Statistical
Reproducibility of Results
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  A high performance profile-biomarker diagnosis for mass spectral profiles.
Next Document:  Combinatorial motif analysis of regulatory gene expression in Mafb deficient macrophages.