Abstract
Multiple testing using DNA microarray gene expression data has revived the promising area of false discovery rate (FDR) in statistics. Some recent advances in FDR controlling procedures can be unified in terms of estimating the proportion of true null hypotheses, π0. In the original FDR procedure π0 was set to its upper bound of one, the most conservative choice. The degree of conservativeness in estimating π0 has a direct impact on the power of FDR procedures to detect true alternative hypotheses. In this work, we examine some recent FDR procedures with respect to the following two primary aims: (1) Compare the conservativeness of estimating π0 (and hence FDR). (2) Evaluate the impact of (1) on the power to detect true alternative hypotheses. We also investigate the sensitivity of FDR procedures to violation of statistical assumptions, such as heterogeneity of variance and independence. The effect of varying sample sizes on the estimation of π0 and power is also explored. Furthermore, in our investigation of aims (1) and (2), we defined and utilized the benchmark FDR procedure. This allows for making absolute power comparisons of FDR procedures to a benchmark, in addition to making relative comparisons among FDR procedures.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 611-637 |
| Number of pages | 27 |
| Journal | Computational Statistics and Data Analysis |
| Volume | 47 |
| Issue number | 3 |
| DOIs | |
| State | Published - Oct 1 2004 |
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Keywords
- Differential gene expression
- DNA Microarray
- False discovery rate
- Multiple hypothesis testing
- p-Value
ASJC Scopus subject areas
- Computational Theory and Mathematics
- Statistics, Probability and Uncertainty
- Electrical and Electronic Engineering
- Computational Mathematics
- Numerical Analysis
- Statistics and Probability
Cite this
On estimating the proportion of true null hypotheses for false discovery rate controlling procedures in exploratory DNA microarray studies. / Nguyen, Danh V.
In: Computational Statistics and Data Analysis, Vol. 47, No. 3, 01.10.2004, p. 611-637.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - On estimating the proportion of true null hypotheses for false discovery rate controlling procedures in exploratory DNA microarray studies
AU - Nguyen, Danh V.
PY - 2004/10/1
Y1 - 2004/10/1
N2 - Multiple testing using DNA microarray gene expression data has revived the promising area of false discovery rate (FDR) in statistics. Some recent advances in FDR controlling procedures can be unified in terms of estimating the proportion of true null hypotheses, π0. In the original FDR procedure π0 was set to its upper bound of one, the most conservative choice. The degree of conservativeness in estimating π0 has a direct impact on the power of FDR procedures to detect true alternative hypotheses. In this work, we examine some recent FDR procedures with respect to the following two primary aims: (1) Compare the conservativeness of estimating π0 (and hence FDR). (2) Evaluate the impact of (1) on the power to detect true alternative hypotheses. We also investigate the sensitivity of FDR procedures to violation of statistical assumptions, such as heterogeneity of variance and independence. The effect of varying sample sizes on the estimation of π0 and power is also explored. Furthermore, in our investigation of aims (1) and (2), we defined and utilized the benchmark FDR procedure. This allows for making absolute power comparisons of FDR procedures to a benchmark, in addition to making relative comparisons among FDR procedures.
AB - Multiple testing using DNA microarray gene expression data has revived the promising area of false discovery rate (FDR) in statistics. Some recent advances in FDR controlling procedures can be unified in terms of estimating the proportion of true null hypotheses, π0. In the original FDR procedure π0 was set to its upper bound of one, the most conservative choice. The degree of conservativeness in estimating π0 has a direct impact on the power of FDR procedures to detect true alternative hypotheses. In this work, we examine some recent FDR procedures with respect to the following two primary aims: (1) Compare the conservativeness of estimating π0 (and hence FDR). (2) Evaluate the impact of (1) on the power to detect true alternative hypotheses. We also investigate the sensitivity of FDR procedures to violation of statistical assumptions, such as heterogeneity of variance and independence. The effect of varying sample sizes on the estimation of π0 and power is also explored. Furthermore, in our investigation of aims (1) and (2), we defined and utilized the benchmark FDR procedure. This allows for making absolute power comparisons of FDR procedures to a benchmark, in addition to making relative comparisons among FDR procedures.
KW - Differential gene expression
KW - DNA Microarray
KW - False discovery rate
KW - Multiple hypothesis testing
KW - p-Value
UR - http://www.scopus.com/inward/record.url?scp=4944260885&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=4944260885&partnerID=8YFLogxK
U2 - 10.1016/j.csda.2004.01.006
DO - 10.1016/j.csda.2004.01.006
M3 - Article
AN - SCOPUS:4944260885
VL - 47
SP - 611
EP - 637
JO - Computational Statistics and Data Analysis
JF - Computational Statistics and Data Analysis
SN - 0167-9473
IS - 3
ER -