References for Microarray Data Analysis

NEW References for Microarray Data Analysis

PubH 5470-2 (Spring 2003)

http://www.biostat.umn.edu/~weip/course/ge/ref02s.html

Introduction to microarray technologies
1. Yeoh E et al. (2002). Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell, 1:133-143. PDF
Measuring gene expression levels
1. Affymetrix (2002). Statistical algorithms description document. PDF
2. WJ Lemon, J.J.T. Palatini, R Krahe and FA Wright (2002). Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays. Bioinformatics, 18: 1470-1476. download
3. Irizarry RA et al. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research, 31: e15. PDF
4. Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003b) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Accepted for publication in Biostatistics. download
5. Y Zhou and R Abagyan (2002). Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics, 3:3. download
6. Kooperberg C et al. (2002). Improved background correction for spotted DNA microarraya. J of Computational Biology, 9: 55-66. download
Data normalization
1. Quackenbush J (2002). Microarray data normalization and transformation. Nature Genetics Supplement, 32, 496-501. download (This is a review article containing other references.)
2. Y. H. Yang, S. Dudoit, P. Luu and T. P. Speed (2001). Normalization for cDNA Microarray Data. SPIE BiOS 2001, San Jose, California, January 2001. download
3. George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao and Wing Hung Wong (2001). Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variation and assessment of gene effects. Nucleic Acids Research, Vol 29, No. 12. 2549-2557. download
4. Eric E. Schadt, Cheng Li, Byron Ellis and Wing H. Wong (2001). Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. Journal of Cellular Biochemistry. Supplement 37, 120-125. download
5. Eric E. Schadt, Cheng Li, Cheng Su, Wing H. Wong (2000). Analyzing high-density oligonucleotide gene expression array data. Journal of Cellular Biochemistry. 80, 192-202. download
6. Bolstad, B.M., Irizarry RA, Astrand, M, and Speed, TP (2003). A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics>/I>. 19(2):185-193. download
7. Durbin, B.P., Hardin, J.S., Hawkins, D.M. and Rocke, D.M. (2002). A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics, 18, S105-S110. download
Detecting differentially expressed genes

Kendziorski, C.M., M.A. Newton, H. Lan, and M.N. Gould (2003). On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Technical Report #166, Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison. Statistics in Medicine (in press). download
M.A. Newton , A. Noueiry, D. Sarkar, and P. Ahlquist (2003). Detecting differential gene expression with a semiparametric hierarchical mixture method. Technical Report #1074, Department of Statistics, UW Madison. download
Cluster analysis

McShane LM, Radmacher MD, Freidlin B, Yu R, Li M-C and Simon R (2002). Methods for assessing reproducibility of clustering patterns observed in analysis of microarray data. Bioinformatics, 18, 1462-1469. download
Tibshirani R, Walther G and Hastie T (2001). Estimating the number of clusters in a data set via the gap statistic. JRSS-B, 63, 411-423.
Dudoit, S. and J. Fridlyand (2002). A prediction-based resampling method to estimate the number of clusters in a dataset. Genome Biology, 3(7), research0036.1 -- 0036.21. download
Classification

Tibshirani, Hastie, Narasimhan and Chu (2002). Diagnosis of multiple cancer types by shrunken centroids of gene expression. PNAS, 99:6567-6572 (May 14). download