Statistical Methods in Bioinformatics - Handouts.

• Handout 1: G. K. Smyth, Y. H. Yang and T. P. Speed Statistical Issues in cDNA Microarray Data Analysis
• Handout 2: Lecture 1
• Handout 3: Lecture 2
• Handout 4: Lecture 3
• Handout 5: Lecture 4
• Handout 6: Lecture 5
• Handout 7: Lecture 6
• Handout 8: Lecture 7
• Handout 9: Lecture 8
• Handout 9a-d: Plots from bagging lecture effect of bagging on tree classification, comparing prediction vote and results of bagging/no bagging for trees, comparing prediction vote and results of bagging/no bagging for kNN, comparing prediction vote and results of bagging/no bagging for knn
• Handout 10: Lecture 9

• Molecular classification of multiple tumor types Bioinformatics 2001 17: S316-S322.
• Gene Selection for Cancer Classification using Support Vector Machines Guyon, Weston, Barnill, M.D., and Vapnik
• Support Vector Machine Classification of Microarray Gene Expression Data Brown, Grundy, Lin, Cristianini, Sugnet, Ares,Jr., and Haussler
• Support vector machine classification and validation of cancer tissue samples using microarray expression data Terrence S. Furey 1,, Nello Cristianini 2, Nigel Duffy 1, David W. Bednarski 3, Michl Schummer 3 and David Haussler 1
• Comparative Study on Feature Selection and Classification Methods Using Gene Expression Profiles Liu, Li, and Wong
• Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Data Lee, and C K Lee
• Multiclass cancer diagnosis using tumor gene expression signatures Ramaswamy, Tamayo, Rifkin, Mukherjee, Yeang, Angelo, Ladd, Reich, Latulippe, Mesirov, Poggio, Gerald, Loda, Lander, and Golub
• Engineering support vector machine kernels that recognize translation initiation sites, A. Zien, G. Rätsch, S. Mika, B. Schölkopf, T. Lengauer, and K.-R. Müller
• Knowledge-based analysis of microarray gene expression data by using support vector machines. Michael P. S. Brown*, William Noble Grundy,, David Lin*, Nello Cristianini§, Charles Walsh Sugnet¶, Terrence S. Furey*, Manuel Ares Jr.¶, and David Haussler*
• Identifying genes related to drug anticancer mechanisms using support vector machine, Lei Bao, Zhirong Sun, FEBS Letters 521 (2002) 109-114.
• guyon
• Multiple testing 1 pdf
• Multiple testing 2pdf
• Clustering pdf
• Clustering 2pdf
• Clustering 3 pdf
• Geneshaving paperTechnical report 2000, Stanford university, Dept of Statistics. Hastie et al

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01/20/03