Analysis of Affymetrix GeneChip® data using amplified RNA

BioTechniques

Volumn 40, Issue 2, 2006, Pages 165-170

  Cope, Leslie ^a   Hartman, Scott M ^b   Göhlmann, Hinrich W H ^c   Tiesman, Jay P ^b   Irizarry, Rafael A ^d  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b PROCTER AND GAMBLE COMPANY   (United States)

^c JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

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

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA REDUCTION; DNA; RNA;

AMPLIFICATION TECHNIQUES; DATA QUALITY; MICRODISSECTION; RANDOM PRIMERS;

GENES;

COMPLEMENTARY DNA; RNA; BACTERIOPHAGE T7 RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; VIRUS PROTEIN;

ALGORITHM; ARTICLE; DATA ANALYSIS; DEVICE; DNA HYBRIDIZATION; GENE AMPLIFICATION; GENETIC TRANSCRIPTION; HUMAN; MICRODISSECTION; RNA ANALYSIS; COMPARATIVE STUDY; DNA MICROARRAY; GENETICS; METHODOLOGY; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID HYBRIDIZATION;

EUKARYOTA;

ALGORITHMS; DNA, COMPLEMENTARY; DNA-DIRECTED RNA POLYMERASES; MICRODISSECTION; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 33645520538     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000112057     Document Type: Article

References (17)

1. King, C., N. Guo, G.M. Frampton, N.P. Gerry, M.E. Lenburg, and C.L. Rosenberg. 2005. Reliability and reproducibility of gene expression measurements using amplified RNA from laser-microdissected primary breast tissue with oligonucleotide arrays. J. Mol. Diagn. 7:57-64.
2. Luzzi, V., M. Mahadevappa, R. Raja, J.A. Warrington, and H.A. Watson. 2005. Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis. J. Mol. Diagn. 5:9-14.
3. Ohyama, H., X. Zhang, Y. Kohno, I. Alevizos, M. Posner, D.T. Wong, and R. Todd. 2000. Laser capture microdissection-generated target sample for high-density oligonucleotide array hybridization. BioTechniques 35:530-536.
4. McClintick, J., R. Jerome, C. Nicholson, D. Crabb, and H. Edenberg. 2003. Reproducibility of oligonucleotide arrays using small samples. BMC Genomics 4:4.
5. Thelen, P., P. Burfeind, M. Grzmil, S. Voigt, R. Ringert, and B. Hemmerlein. 2004. cDNA microarray analysis with amplified RNA after isolation of intact cellular RNA from neoplastic and non-neoplastic prostate tissue separated by laser microdissections. Int. J. Oncol. 24:1085-1092.
6. Gomes, L., R. Silva, B. Stolf, E. Cristo, R. Hirata, F. Soares, L. Reis, E. Neves, and A. Carvalho. 2003. Comparative analysis of amplified and nonamplified RNA for hybridization in cDNA microarray. Anal. Biochem. 321:244-251.
7. Jenson, S.D., R.S. Robetorye, S.D. Bohling, J.A. Schumacher, J.W. Morgan, M.S. Lim, and K.S.J. Elenitoba-Johnson. 2003. Validation of cDNA microarray gene expression data obtained from linearly amplified RNA. Mol. Pathol. 56:307-312.
8. Klur, S., K. Toy, M.P. Williams, and U. Certa. 2004. Evaluation of procedures for amplification of small-size samples for hybridization on microarrays. Genomics 83:508-517.
9. Singh, R., R.J. Maganti, S.V. Jabba, M. Wang, G. Deng, J.D. Heath, N. Kurn, and P. Wangemann. 2005. Microarray-based comparison of three amplification methods for nanogram amounts of total RNA. Am. J. Physiol. Cell Physiol. 288:1179-1189.
10. Li, C. and W.H. Wong. 2001. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98:31-36.
11. Irizarry, R.A., B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, and T.P. Speed. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264.
12. Hoaglin D.C., F. Mosteller, and J.W. Tukey. 2000. Understanding Robust and Exploratory Data Analysis. John Wiley & Sons, New York.
13. Bolstad, B.M., F. Collin, J. Brettschneider, K. Simpson, L. Cope, R.A. Irizarry, and T.P. Speed. 2005. Quality assessment of Affymetrix, p. 33-49. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber (Eds.), Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York.
14. R Development Core Team. 2004. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
15. Gentleman, R.C., V.J. Carey, D.M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, et al. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R80.
16. Irizarry R.A., D. Warren, F. Spencer, I.F. Kim, S. Biswal, B.C. Frank, E. Gabrielson, J.G.N. Garcia, et al. 2005. Multiple-laboratory comparison of microarray platforms. Nat. Methods 2:345-350.
17. Smyth, G.K. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3:3.