Removing technical variability in RNA-seq data using conditional quantile normalization

Biostatistics

Volumn 13, Issue 2, 2012, Pages 204-216

  Hansen, Kasper D ^a   Irizarry, Rafael A ^a   Wu, Zhijin ^b  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b BROWN UNIVERSITY   (United States)

Author keywords

Gene expression; Normalization; RNA sequencing

Indexed keywords

ALGORITHM; ANALYSIS OF VARIANCE; ARTICLE; BIOSTATISTICS; COMPARATIVE STUDY; DNA BASE COMPOSITION; DNA MICROARRAY; EVALUATION; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SEQUENCING; HUMAN; NUCLEIC ACID DATABASE; SEQUENCE ANALYSIS; STATISTICS;

ALGORITHMS; ANALYSIS OF VARIANCE; BASE COMPOSITION; BIOSTATISTICS; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, RNA;

EID: 84858068675     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxr054     Document Type: Article

References (38)

1. AIRD, D., ROSS, M. G., CHEN, W.-S., DANIELSSON, M., FENNELL, T., RUSS, C., JAFFE, D. B., NUSBAUM, C. AND GNIRKE, A. (2011). Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biology 12, R18.
2. ANDERS, S. AND HUBER, W. (2010). Differential expression analysis for sequence count data. Genome Biology 11, R106.
3. BOLSTAD, B. M., IRIZARRY, R. A., Å STRAND, M. AND SPEED, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193. (Pubitemid 36181903)
4. BOTTOMLY, D., WALTER, N. A. R., HUNTER, J. E., DARAKJIAN, P., KAWANE, S., BUCK, K. J., SEARLES, R. P., MOONEY, M., MCWEENEY, S. K. AND HITZEMANN, R. (2011). Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-seq and microarrays. PloS One 6, e17820.
5. BULLARD, J. H., PURDOM, E., HANSEN, K. D. AND DUDOIT, S. (2010). Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11, 94.
6. CARVALHO, B., BENGTSSON, H., SPEED, T. P. AND IRIZARRY, R. A. (2007). Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8, 485.
7. CHEUNG, V. G., NAYAK, R. R., WANG, I. X., ELWYN, S., COUSINS, S. M., MORLEY, M. AND SPIELMAN, R. S. (2010). Polymorphic cis-and trans-regulation of human gene expression. PLoS Biology 8, e1000480.
8. DOHM, J. C., LOTTAZ, C., BORODINA, T. AND HIMMELBAUER, H. (2008). Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research 36, e105.
9. EVELAND, A. L., SATOH-NAGASAWA, N., GOLDSHMIDT, A., MEYER, S., BEATTY, M., SAKAI, H., WARE, D. AND JACKSON, D. (2010). Digital gene expression signatures for maize development. Plant physiology 154, 1024.
10. FLICEK, P., AMODE, M. R., BARRELL, D., BEAL, K., BRENT, S., CHEN, Y., CLAPHAM, P., COATES, G., FAIRLEY, S., FITZGERALD, S. and others (2011). Ensembl 2011. Nucleic Acids Research 39 (Suppl 1), D800.
11. HANSEN, K. D., BRENNER, S. E. AND DUDOIT, S. (2010). Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research 38, e131.
12. HANSEN, K. D., WU, Z., IRIZARRY, R. A. AND LEEK, J. T. (2011). Sequencing technology does not eliminate biological variability. Nature Biotechnology 29, 572-573.
13. INTERNATIONAL HAPMAP CONSORTIUM (2003). The International HapMap Project. Nature 426, 789-796.
14. KOENKER, R. (2005). Quantile Regression. New York: Cambridge University Press.
15. LANGMEAD, B., HANSEN, K. D. AND LEEK, J. T. (2010). Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology 11, R83.
16. LANGMEAD, B., TRAPNELL, C., POP, M. AND SALZBERG, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10, R25.
17. LEFEBVRE, G., DESFARGES, S., UYTTEBROECK, F., MUNOZ, M., BEERENWINKEL, N., ROUGEMONT, J., TELENTI, A. AND CIUFFI, A. (2011). Analysis of HIV-1 expression level and sense of transcription by highthroughput sequencing of the infected cell. Journal of Virology 85, 6205-6211.
18. LI, J., JIANG, H. AND WONG, W. H. (2010). Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biology 11, R50.
19. MAQC CONSORTIUM (2006). The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 24, 1151-1161.
20. MARIONI, J. C., MASON, C. E., MANE, S. M., STEPHENS, M. AND GILAD, Y. (2008). RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 18, 1509-1517.
21. MCCARTHY, D. J., CHEN, Y. AND SMYTH, G. K. (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation Nucleic Acids Research (in press).
22. MONTGOMERY, S. B., SAMMETH, M., GUTIERREZ-ARCELUS, M., LACH, R. P., INGLE, C., NISBETT, J., GUIGO, R. AND DERMITZAKIS, E. T. (2010). Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-777.
23. MORTAZAVI, A., WILLIAMS, B. A., MCCUE, K., SCHAEFFER, L. AND WOLD, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-628. (Pubitemid 351911867)
24. NAEF, F. AND MAGNASCO, M. O. (2003). Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. Physical Review E 68, 011906.
25. NANNYA, Y., SANADA, M., NAKAZAKI, K., HOSOYA, N., WANG, L., HANGAISHI, A., KUROKAWA, M., CHIBA, S., BAILEY, D. K., KENNEDY, G. C. and others (2005). A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Research 65, 6071.
26. PAI, A. A., BELL, J. T., MARIONI, J. C., PRITCHARD, J. K. AND GILAD, Y. (2011). A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genetics 7, e1001316.
27. PICKRELL, J. K., MARIONI, J. C., PAI, A. A., DEGNER, J. F., ENGELHARDT, B. E., NKADORI, E., VEYRIERAS, J.-B., STEPHENS, M., GILAD, Y. AND PRITCHARD, J. K. (2010). Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768-772.
28. ROBERTS, A., TRAPNELL, C., DONAGHEY, J., RINN, J. L. AND PACHTER, L. (2011). Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology 12, R22.
29. ROBINSON, M. D., MCCARTHY, D. J. AND SMYTH, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140.
30. ROBINSON, M. D. AND OSHLACK, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11, R25.
31. ROBINSON, M. D. AND SMYTH, G. K. (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887. (Pubitemid 350162894)
32. ROBINSON, M. D. AND SMYTH, G. K. (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9, 321-332. (Pubitemid 351438556)
33. TRAPNELL, C., WILLIAMS, B. A., PERTEA, G., MORTAZAVI, A., KWAN, G., VAN BAREN, M. J., SALZBERG, S. L., WOLD, B. J. AND PACHTER, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28, 511-515.
34. WANG, Z., GERSTEIN, M. AND SNYDER, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10, 57-63.
35. WU, Z. AND ARYEE, M. J. (2010). Subset quantile normalization using negative control features. Journal of Computational Biology 17, 1385-1395.
36. WU, Z., IRIZARRY, R. A., GENTLEMAN, R., MARTINEZ-MURILLO, F. AND SPENCER, F. (2004). A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association 99, 909-917. (Pubitemid 39665934)
37. WU, Z. J., MEYER, C. A., CHOUDHURY, S., SHIPITSIN, M., MARUYAMA, R., BESSARABOVA, M., NIKOLSKAYA, T., SUKUMAR, S., SCHWARTZMAN, A., LIU, J. S. and others (2010). Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Research 20, 1730.
38. ZHANG, L., MILES, M. F. AND ALDAPE, K. D. (2003). A model of molecular interactions on short oligonucleotide microarrays. Nature Biotechnology 21, 818-821. (Pubitemid 36791403)