Statistical implications of pooling RNA samples for microarray experiments

BMC Bioinformatics

Xuejun Peng¹  Constance L Wood¹  Eric M Blalock²  Kuey Chu Chen²  Philip W Landfield²  Arnold J Stromberg¹ 

[1] Department of Statistics, University of Kentucky, Lexington, KY 40506, USA

[2] Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, KY 40536, USA

关键词: Sample size estimation;    Power;    Pooling;    Replicates;    Microarray experiment design;   

Others  :  1171885
DOI  :  10.1186/1471-2105-4-26

 received in 2002-12-02, accepted in 2003-06-24,  发布年份 2003

【 摘 要 】

Background

Microarray technology has become a very important tool for studying gene expression profiles under various conditions. Biologists often pool RNA samples extracted from different subjects onto a single microarray chip to help defray the cost of microarray experiments as well as to correct for the technical difficulty in getting sufficient RNA from a single subject. However, the statistical, technical and financial implications of pooling have not been explicitly investigated.

Results

Modeling the resulting gene expression from sample pooling as a mixture of individual responses, we derived expressions for the experimental error and provided both upper and lower bounds for its value in terms of the variability among individuals and the number of RNA samples pooled. Using "virtual" pooling of data from real experiments and computer simulations, we investigated the statistical properties of RNA sample pooling. Our study reveals that pooling biological samples appropriately is statistically valid and efficient for microarray experiments. Furthermore, optimal pooling design(s) can be found to meet statistical requirements while minimizing total cost.

Conclusions

Appropriate RNA pooling can provide equivalent power and improve efficiency and cost-effectiveness for microarray experiments with a modest increase in total number of subjects. Pooling schemes in terms of replicates of subjects and arrays can be compared before experiments are conducted.

【 授权许可】

   
2003 Peng et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.

【 图 表 】

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