Effect of pooling samples on the efficiency of comparative studies using microarrays

Bioinformatics

Volumn 21, Issue 24, 2005, Pages 4378-4383

  Zhang, Shu Dong ^a   Gant, Timothy W ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOMEDICAL TECHNOLOGY ASSESSMENT; CALCULATION; COMPARATIVE STUDY; COST EFFECTIVENESS ANALYSIS; DNA MICROARRAY; EXPERIMENTAL DESIGN; GENE EXPRESSION; MATHEMATICAL MODEL; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; SAMPLING;

EID: 28944441103     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti717     Document Type: Article

References (19)

1. Affymetrix (2004), Sample pooling for microarray analysis. Technical note, Affymetrix, San Diego.
2. Agrawal,D. et al. (2002) Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling. J. Natl Cancer Inst., 94, 513-521.
3. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
4. Brownlee,K.A. (1965) Statistical Theory and Methodology in Science and Engineering. John Wiley and Sons, Inc., New York.
5. Churchill,G.A. and Oliver,B. (2001) Sex, flies and microarrays. Nat. Genet., 29, 355-356.
6. Dorfman,R. (1943) The detection of defective members of large populations. Ann. Math. Stat., 14, 436-440.
7. Efron,B. (2004) Large-scale simultaneous hypothesis testing: The choice of a null hypothesis. J. Am. Stat. Assoc., 99, 96-104.
8. Gastwirth,J.L. (2000) The efficiency of pooling in the detection of rare mutations. Am. J. Hum. Genet., 67, 1036-1039.
9. Grant,G.R. et al. (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Bioinformatics, 21, 2684-2690.
10. Jin,W. et al. (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet., 29, 389-395.
11. Jolly,R.A. et al. (2005) Pooling samples within microarray studies: A comparative analysis of rat liver transcription response to prototypical toxicants. Physiol Genomics, 22, 346-355.
12. Kendziorski,C. et al. (2005) On the utility of pooling biological samples in microarray experiments. Proc. Natl Acad. Sci. USA, 102, 4252-4257.
13. Kendziorski,C.M. et al. (2003) The efficiency of pooling mRNA in microarray experiments. Biostatistics, 4, 465-477.
14. Muckenthaler,M. et al. (2003) Regulatory defects in liver and intestine implicate abnormal hepcidin and Cybrd1 expression in mouse hemochromatosis. Nat. Geneti., 34, 102-107.
15. Peng,X. et al. (2003) Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics, 4, 26.
16. Pounds,S. and Morris,S.W. (2003) Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics, 19, 1236-1242.
17. Shih,J.H. et al. (2004) Effects of pooling mRNA in microarray class comparisons. Bioinformatics, 20, 3318-3325.
18. Storey,J.D. and Tibshirani,R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA, 100, 9440-9445.
19. Zhang,S.-D. and Gant,T.W. (2004) A statistical framework for the design of microarray experiments and effective detection of differential gene expression. Bioinformatics, 20, 2821-2828.