Evaluation of Statistical Methods for Assessment of Agreement for Gene Expression Data from Microarray Experiments
Date Issued
2006
Date
2006
Author(s)
Lin, Chia-Ying
DOI
en-US
Abstract
Microarray is one of the breakthrough technologies in the twenty first century. Despite of its great potentials, the transition and realization of microarray technology into the clinically useful commercial products has not been as rapid as the technology could promise. Only recently, the US Food and Drug Administration (FDA) approved the first biochip product based on the microarray technology. One of the primary reasons is lack of agreement and poor reproducibility of the intensity measurements on gene expression obtained from microarray experiments. As a result, agreement and reproducibility have recently drawn a lot of attention in microarray experiments. Current practices often use the Pearson’s correlation coefficient to assess the agreement of expression data between the technical replicates from microarray experiments. However, Pearson’s correlation coefficient is to evaluate association between two variables and is not appropriate for evaluation of agreement of expression levels of the same gene between technical replicates. Therefore, we propose to use the concordance correlation coefficient (CCC) to assess agreement of expression levels of the same gene between technical replicates. We also apply the Generalized Pivotal Quantities (GPQ) to obtain the exact confidence interval for concordance correlation coefficient. In addition, a one-side (1-α) lower confidence limit for ρc is employed to test the hypothesis that agreement of expression levels of the same gene between two laboratories exceeds some minimal requirement of agreement. We conducted a simulation study, under various combinations of mean differences, variability, and sample size, to empirically compare the performance of different methods for assessment of agreement in terms of coverage probability, expected length, size, and power. Numeric data from published papers illustrate the applications of the proposed methods.
Subjects
一致性
相等性
一致性相關係數
廣義的樞紐量
方法比較
Agreement
Equivalence
Concordance correlation coefficient
Generalized pivotal quantity
Method comparison
Type
thesis