Introduction to R and Statistical Data Analysis

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1 Microarray Center Introduction to R and Statistical Data Analysis PART II Petr Nazarov petr.nazarov@crp-sante.lu

2 OUTLINE PART II Descriptive statistics in R (8) sum, mean, median, sd, var, cor, etc. Principle component analysis and clustering (9) PCA, k-means clustering, hierarchical clustering Random numbers (10) random number generators, distributions Statistical tests (11) t-test, Wilcoxon test, multiple test correction. ANOVA and Linear regression (12) ANOVA, linear regression Look Look for for corresponding scripts scripts at at

3 8. DESCRIPTIVE STATISTICS IN R Center, Variation, Dependency

4 9. PCA AND CLUSTERING 9.1. Iris Data from R.A.Fisher The Iris flower data set or Fisher's Iris data set is a multivariate data set introduced by Sir Ronald Aylmer Fisher (1936) as an example of discriminant analysis. It is sometimes called Anderson's Iris data set because Edgar Anderson collected the data to quantify the geographic variation of Iris flowers in the Gaspé Peninsula. The dataset consists of 50 samples from each of three species of Iris flowers (Iris setosa, Iris virginica and Iris versicolor). Four features were measured from each sample, they are the length and the width of sepal and petal, in centimeters. Based on the combination of the four features, Fisher developed a linear discriminant model to distinguish the species from each other. Iris setosa Iris versicolor Iris virginica

5 9. PCA AND CLUSTERING 9.1. Data Presentation iris str(iris) ## plot iris data x11() plot(iris[,-5]) plot(iris[,-5], col = iris[,5]) Sepal.Length Sepal.Width Petal.Length Petal.Width

6 9. PCA AND CLUSTERING 9.2 Principle Component Analysis (PCA) Principal Principal component component analysis analysis (PCA) (PCA) is is a vector vector space space transform transform used used to to reduce reduce multidimensional multidimensional data data sets sets to to lower lower dimensions dimensions for for analysis. analysis. It It selects selects the the coordinates coordinates along along which which the the variation variation of of the the data data is is bigger. bigger genes 2 dimensions For the simplicity let us consider 2 parametric situation both in terms of data and resulting PCA. Scatter plot in natural coordinates Scatter plot in PC Variable 2 Second component Variable 1 First component Instead of using 2 natural parameters for the classification, we can use the first component! nt!

7 9. PCA AND CLUSTERING 9.2. Data Transformation for PCA Data = as.matrix(iris[,-5]) row.names(data) = as.character(iris[,5]) classes = as.integer(iris[,5]) ## plot data in 3d library(scatterplot3d) x11() scatterplot3d(iris[,1],iris[,2],iris[,3], pch=19,color=classes, main = "Iris", xlab = names(iris)[1], ylab = names(iris)[2], zlab = names(iris)[3]) legend(4,7,levels(iris$species), col=c(1,2,3),pch=19) Petal.Length setosa versicolor virginica Iris Sepal.Width Sepal.Length

8 9. PCA AND CLUSTERING 9.2. PCA

9 9. PCA AND CLUSTERING 9.3. k-means Clustering k-means k-means Clustering Clustering k-means k-means clustering clustering is is a method method of of cluster cluster analysis analysis which which aims aims to to partition ppartition n observations observations into into k k clusters clusters in in which which each each observation observation belongs belongs to to the the cluster clusterwith with the the nearest nearest mean. mean. 1) k initial "means" (in this case k=3) are randomly selected from the data set (shown in color). 2) k clusters are created by associating every observation with the nearest mean. 3) The centroid of each of the k clusters becomes the new means. 4) Steps 2 and 3 are repeated until convergence has been reached.

10 clusters = kmeans(x=data,centers=3,nstart=10)$cluster x11() plot(pc$x[,1],pc$x[,2],col = classes,pch=clusters) legend(2,1.4,levels(iris$species),col=c(1,2,3),pch=19) legend(-2.5,1.4,c("c1","c2","c3"),col=4,pch=c(1,2,3)) 9. PCA AND CLUSTERING 9.3. k-means Clustering PC$x[, 2] c1 c2 c3 setosa versicolor virginica PC$x[, 1]

11 9. PCA AND CLUSTERING 9.4. Hierarchical Clustering Hierarchical Hierarchical Clustering Clustering Hierarchical Hierarchical clustering clustering creates creates a hierarchy hierarchy of of clusters clusters which which may may y be be represented represented in in a tree tree structure structure called called a dendrogram. dendrogram. The The root root of of the the tree tree consists consists of of a single single cluster cluster containing containing all all observations, observations, and and the the leaves leaves correspond correspond to to individual individual observations. observations. Algorithms Algorithms for for hierarchical hierarchical clustering clustering are are generally generally either either agglomerative, agglomerative,, in in which which one one starts starts at at the the leaves leaves and and successively successively merges merges clusters clusters together; together; or or divisive, divisive,, in in which which one one starts starts at at the the root root and and recursively recursively splits splits the the clusters. clusters. Elements Agglomerative Divisive Dendrogram Distance: Euclidean

12 9. PCA AND CLUSTERING 9.4. Hierarchical Clustering ## use heatmap heatmap(data) ## use heatmap with colors color = character(length(classes)) color[classes == 1] = "black" color[classes == 2] = "red" color[classes == 3] = "green" heatmap(data,rowsidecolors=color) Iris setosa Iris versicolor Iris virginica

13 9. PCA AND CLUSTERING 9.5. Example: Task 8a Acute lymphoblastic leukemia (ALL), is a form of leukemia, or cancer of the white blood cells characterized by excess lymphoblasts. all_data.xls contains the results of full-trancript profiling for ALL patients and healthy donors using Affymetrix microarrays. The data were downloaded from ArrayExpress repository and normalized. The expression values in the table are in log 2 scale.

14 10. RANDOM NUMBERS AND DISTRIBUTIONS See Source Code

15 11. STATISTICAL TESTS See Source Code

16 12. ANOVA and LINEAR REGRESSION Why ANOVA? Means for for more than 2 populations We We have measurements for for 5 conditions. Are Are the the means for for these conditions equal? If we would use pairwise comparisons, what will be the probability of getting error? 5 5! Number of comparisons: C2 = = 10 2!3! Probability of an error: : 1 (0.95) 1 10 = 0.4 Validation of of the the effects We We assume that that we we have several factors affecting our our data. Which factors are are most significant? Which can can be be neglected? ANOVA example from Partek

17 12. ANOVA and LINEAR REGRESSION Meaning of ANOVA H 0 : 0 : µ 1 = 1 µ 2 = 2 µ 3 3 H a : a : not not all all 3 means means are are equal equal Depression level m 1 m 2 m Measures

18 12. ANOVA and LINEAR REGRESSION ANOVA in R: Fast and Simple salaries.txt

19 12. ANOVA and LINEAR REGRESSION Regression Model and Regression Line Regression Regression model model The The equation equation describing describing how how y y is is related related to to x x and and an an error error term; term; in in simple simple linear linear regression, regression, the the regression regression model model is is y = β 0 β + 0 β 1 βx 1 + εε Regression Regression equation equation The The equation equation that that describes describes how how the the mean mean or or expected expected value value of of the the dependent dependent variable variable is is related related to to the the independent independent variable; variable; in in simple simple linear linear regression, regression, E(y) E(y) =β =β β 1 βx 1 Number of cells Temperature Model for a simple linear regression: y( x) β x + β + ε = 1 0

20 12. ANOVA and LINEAR REGRESSION Comparison of ANOVA and Linear Regression Depression level m 1 m 2 m 3 Number of cells Measures Temperature SST = SSTR + SSE SST = SSR + SSE

21 12. ANOVA and LINEAR REGRESSION Linear Regression in R cells.txt y x

22 REGRESSION ANALYSIS Solution of Task 12 leukemia.txt Survival data1$survival data1$wbc

23 Thank you for your attention Questions?

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