Publication

Meta-analysis of incomplete microarray studies

Abstract

Meta-analysis of microarray studies to produce an overall gene list is relatively straightforward when complete data are available. When some studies lack information, for example, having only a ranked list of genes instead of complete primary data, it is common to reduce all studies to ranked lists prior to combining them. Since this entails a loss of information, we consider a hierarchical Bayes modeling approach to combining studies using the type of information available in each study: the full data matrix, summary statistics, or ranks for each gene. The model uses an informative prior for the parameter of interest, which eases the detection of differentially expressed genes. Simulations show that the new approach can give substantial power gains compared to classical meta analysis and list aggregation. A large meta-analysis based on 11 published studies providing data of the types cited above is also performed and shows credible results by identifying genes known to be involved in ovarian cancer.

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Related concepts (37)
Summary statistics
In descriptive statistics, summary statistics are used to summarize a set of observations, in order to communicate the largest amount of information as simply as possible. Statisticians commonly try to describe the observations in a measure of location, or central tendency, such as the arithmetic mean a measure of statistical dispersion like the standard mean absolute deviation a measure of the shape of the distribution like skewness or kurtosis if more than one variable is measured, a measure of statistical dependence such as a correlation coefficient A common collection of order statistics used as summary statistics are the five-number summary, sometimes extended to a seven-number summary, and the associated box plot.
Bayesian statistics
Bayesian statistics (ˈbeɪziən or ˈbeɪʒən ) is a theory in the field of statistics based on the Bayesian interpretation of probability where probability expresses a degree of belief in an event. The degree of belief may be based on prior knowledge about the event, such as the results of previous experiments, or on personal beliefs about the event. This differs from a number of other interpretations of probability, such as the frequentist interpretation that views probability as the limit of the relative frequency of an event after many trials.
DNA microarray
A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles (10−12 moles) of a specific DNA sequence, known as probes (or reporters or oligos). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target) under high-stringency conditions.
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