Systems Biology
Name:
Student ID:
1. Save the following data in a text file called “DataGE1.txt” in the working directory
of your R programming and Cluster the multivariate data using R by PCA analysis
based on first two principal components. Compare the results obtained by
hierarchical clustering in homework 2.
name
G1
G2
G3
G4
G5
G6
G7
G8
G9
G10
EX1
10
10
4
9.5
4.5
10.5
5
2.7
9.7
10.2
EX2
8
0
8.5
0.5
8.5
9
8.5
8.7
2.0
1.0
EX3
10
9
3
8.5
2.5
12
11
2.0
9.0
9.2
Tentative simple R commands are as follows:
data <- read.table("DataGE1.txt", header=T, row.names="name")
PCAResult <- princomp(data,cor=TRUE)
summary(PCAResult)
biplot(PCAResult,scale=0,cex=c(0.5,0.5))
2. Try to run the following commands on R and print and explain the results.
x <- rbind(matrix(rnorm(60, mean = 1, sd
matrix(rnorm(60, mean = 5, sd
matrix(rnorm(60, mean =10, sd
colnames(x) <- c("A", "B")
cl <- kmeans(x, 3)
plot(x, col = cl$cluster)
points (cl$centers, col = 1:3, pch = 10,
= 0.4), ncol = 2),
= 0.3), ncol = 2),
= 0.5), ncol = 2))
cex=2)
3. Draw the 2-kore subgraph of the following graph on the right side.
4.
5.
Draw the highest k-kore of the following graph on the right side.
Calculate Betweenness and Eigenvector centralities of the nodes of the following
grapg using CentiBiN: