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Advanced course for R-based microarray data analysis

Robert Gentleman & Jean Yee Hwa Yang

October 12-15, 2004

KTH – Royal Institute of Technology, Albanova University Center, Stockholm, Sweden

 

Here are some references for course. 

References: 

Software:

 

General:

bullet DNA Microarrays: A Molecular Cloning Manual.  In D. Bowtell and J. Sambrook (eds),  Cold Spring Harbor Press. [CSHL]
bullet G. K Smyth, Y. H. Yang, T. P. Speed (2003). Statistical issues in microarray data analysis. In: Functional Genomics: Methods and Protocols, M. J. Brownstein and A. B. Khodursky (eds.), Methods in Molecular Biology Volume 224, Humana Press, Totowa, NJ, pages 111-136. [pdf]
bulletBook: "Statistical analysis of gene expression microarray data", edited by Terry Speed, CRC Press, 2003.
bulletBook: "Microarrays for an integrative genomics" by Issac Kohane, Alvin Kho and Atul Butte, MIT Press, 2002.
bulletP. Sebastiani, E. Gussoni, I. S. Kohane and M. Ramoni, (2003), Statistical Challenges in Functional Genomics. (With discussion) Statistical Science. To appear.

Web links:

bullet Standford Web site: Complete guide to “microarraying”
bullet http://www.microarrays.org  -Parts and assembly instructions for printer and scanner.
bullet Animation: http://www.bio.davidson.edu/courses/genomics/chip/chip.html

Data repository:

bulletBrazma et al (2003) ArrayExpress--a public repository for microarray gene expression data at the EBI.  Nucleic Acids Research Jan 1; Vol. 31, No. 1, pp.68-71 [pubmed]

Microarray Techonology:

bulletYuen et al (2002). Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Research, Vol. 30, No.10, e48 [pubmed]
bulletTaniguchi et al (2001). Quantitative assessment of DNA microarrays--comparison with Northern blot analyses. Genomics, Jan 1; Vol. 71, No. 1, pp: 34--39. [pubmed]
bulletJ. Li, M. Pankratz and J. Johnson (2002) Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicology Science Oct; Vol. 69 No. 2, pp.383--390. [pubmed]
Yue et al. (2001) An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Research 2001 Apr 15;29(8):E41-1. [pubmed]
bulletHolloway et al (2002) Options available--from start to finish--for obtaining data from DNA microarrays II. Nature Genetics Dec; Vol 32 Suppl:481-9. [Journal website]

Preprocessing : Image analysis & Normalization

    Image Analysis:

bulletJ. Angulo and J. Serra (2003) Automatic analysis of DNA microarray images using mathematical morphology. Bioinformatics Vol. 19, pp 553--562. [pdf]
bulletY. H. Yang, M. J. Buckley, S. Dudoit, and T. P. Speed (2002). Comparison of methods for image analysis on cDNA microarray data. Journal of Computational and Graphical Statistics, Vol. 11, No. 1, pp. 108--136. [UCB Tech report #584].

    Two-colors normalization

bulletY. H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, Vol. 30, No. 4, e15. [Journal website] [pdf].
bulletJ. van de Peppel, P. Kemmeren, H. van Bakel, M. Radonjic, D. van Leenen, F.C.P. Holstege.  Monitoring global mRNA changes with externally controlled microarray experiments. Embo Reports 4: 387-393 (2003).

    Affy and Single-channel normalization

bullet Y. H. Yang and N. Thorne (2003) Normalization for Two-color cDNA Microarray Data. Science and Statistics: A Festschrift for Terry Speed, D. Goldstein (eds.),  IMS Lecture Notes, Monograph Series, Vol 40, pp. 403--418. [pdf]
bulletHuber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 2002. 18 Suppl 1, S96-104.
bulletBolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193 Supplemental information
bulletRafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15

Experimental Design

bullet Y. H. Yang and T. P. Speed (2002) Design issues for cDNA microarray experiments. Nature Review Genetics Vol. 3, pp. 579--558. [Journal's Web] [pdf]
bulletT. P. Speed and Y. H Yang (2002). Direct versus indirect designs for cDNA microarray experiments. Sankhya : The Indian Journal of Statistics, Vol. 64, Series A, Pt. 3, pp 706-720. [Journal's Web] [pdf]
bulletG. Glonek and P. Solomon (2002) Factorial designs for microarray experiments.  Techinical Report, Department of applied Mathematics, University of Adelaide.
bulletK. Kerr and G. Churchill (2001). Experimental design for gene expression microarrays.  Biostatistics, 2, 182-201.

Differential Gene Expression, Clustering & Discrimination

    see technical reports and published papers on statistical analysis of microarray experiments maintained by Gordon Smyth.

Last Updated: 2004/09/26 20:03