Affymetrix Analysis

Readings from Irizarry's papers (among others):

Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics. Vol. 4, Number 2: 249-264. [Abstract, PDF, PS, Complementary Color Figures-PDF, Software,]

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. 19(2):185-193. (Bioinformatics is available from the PSU library site).

2-channel Array Analysis

Terry Speed's Lab

Readings from Speed's papers

Y. H. Yang, S. Dudoit, P. Luu and T. P. Speed. Normalization for cDNA Microarray Data. SPIE BiOS 2001, San Jose, California, January 2001.

Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide http://nar.oxfordjournals.org/cgi/content/full/30/4/e15

Readings from Altman

N. S. Altman (2005) Replication, Variation and Normalization in Microarray Experiments. Applied Bioinformatics, 4, 33-44.

ANOVA and Related Methods

P. Baldi and A.D. Long, "A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes", Bioinformatics, 17, 6, 509-519, (2001).

Efron, 2005, Large-Scale Simultaneous Hypothesis Testing: The Choice of A Null Hypothesis

Ishwaran, H. and Rao, J.S. (2003). Detecting differentially expressed genes in microarrays using Bayesian model selection. J. Amer. Stat. Assoc., 98, 438-455. pdf

I. Lonnstedt and T. P. Speed. Replicated Microarray Data. Statistical Sinica, Accepted. [ps] [pdf]

Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. _Statistical Applications in Genetics and Molecular Biology_, *3*,No. 1, Article 3.

Tusher, Tibshirani and Chu (2001):
"Significance analysis of microarrays applied to the ionizing radiation response" (ps file). (pdf version). PNAS 2001 98: 5116-5121

Multiple Comparisons

Allison, D. B., Gadbury, G. L., Heo, M., Fernández, J., Lee, K-C., Prolla, T. A, Weindruch, R. (2002). A Mixture Model Approach for the Analysis of Microarray Gene Expression Data. Computational Statistics & Data Analysis, 39, 1-20.

Benjamini Y, Yekutieli D
The control of the false discovery rate in multiple testing under dependency
ANN STAT 29 (4): 1165-1188 AUG 2001

Efron, 2005, Large-Scale Simultaneous Hypothesis Testing: The Choice of A Null Hypothesis

Storey and Tibshirani (2003) Statistical significance for genomewide studies

Experimental Design

Kerr and Churchill (2001), Experimental design for gene expression microarrays, Biostatistics, 2:183-201.

Design of Studies Using cDNA Microarrays. Simon, Radmacher and Dobbin, 2002 Genetic Epidemiology, 23(1): 21-26.

DESIGN ISSUES FOR CDNA MICROARRAY EXPERIMENTS Yee Hwa Yang & Terry Speed Nature Reviews Genetics 3, 579 -588 (2002)

Caldo, R. A., Nettleton, D., Wise, R. P. (2004). Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. The Plant Cell. 16 2514-2528.