PPT-Xuhua Xia

Slide 1 Correlation Simple correlation between two variables Multiple and Partial correlations between one variable and a set of other variables Canonical Correlation between two sets of variables each containing more than one variable. Fitting Several Regression Lines. Many applications of statistical analysis involves a continuous variable as dependent variable (DV) but both continuous and categorical variables as independent variables (IV). . Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Normal and Thalassemia HBb. Are the two genes homologous?. What evolutionary change can you infer from the alignment? . What is the consequence of the evolutionary change?. Stepwise Regression. Y may depend on many independent variables. How to find a subset of X’s that best predict Y?. There are several criteria (e.g., adjusted R. 2. , AIC, BIC, likelihood ratio test, etc.) for model selection and many algorithms for including or excluding X’s in the model: forward selection, backward elimination, stepwise regression, etc.. Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Normal and Thalassemia HBb. Are the two genes homologous?. What evolutionary change can you infer from the alignment? . What is the consequence of the evolutionary change?. Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Lecture Outline. Objectives in this lecture. Grasp the basic concepts distance-based tree-building algorithms. Learn the least-squares criterion and the minimum evolution criterion and how to use them to construct a tree. Xuhua Xia. xxia@uottawa.ca. http://. dambe.bio.uottawa.ca. Xuhua Xia. Transition bias refers to the degree by which the s/v ratio deviates from the expected 1/2. The observed s/v ratio is almost always much larger than 1/2.. Many applications of statistical analysis involves a continuous variable as dependent variable (DV) but both continuous and categorical variables as independent variables (IV). . Relationship between DV and continuous IVs is linear and the slope remains the same in different groups: ANCOVA.. Least-squares, Maximum likelihood and Bayesian methods Xuhua Xia xxia@uottawa.ca http://dambe.bio.uottawa.ca Bayesian inference: Basic terms Conditional probability, e.g., p(P|C) = 10/100 Joint probability Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Normal and Thalassemia HBb. Are the two genes homologous?. What evolutionary change can you infer from the alignment? . What is the consequence of the evolutionary change?. Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Normal and Thalassemia HBb. Are the two genes homologous?. What evolutionary change can you infer from the alignment? . What is the consequence of the evolutionary change?. http://dambe.bio.uottawa.ca. Slide . 2. Causes of genomic evolution. Variation in genome size and gene content. sequence duplication (genome, segmental, gene). horizontal gene transfer. transposition (Barbara McClintock). xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Definitions. Genome: the . entire complement of genetic material carried by an individual. Transcriptome with two definitions:. the . entire set of . transcribable sequences from the genome (operationally all RNA sequences from annotated productive genes in a genome). PCA: principal component analysis. Correspondence analysis. Canonical correlation. Discriminant function analysis. Cluster analysis. MANOVA. PCA. Given a set of variables . x. 1. , . x. 2. , …, . x.