# your code goes here
library(GEOquery)
library("ALL")
gse <- getGEO("GSE189086", GSEMatrix=TRUE,AnnotGPL = TRUE)
length(gse)
gse<-gse[[1]]
Data<-exprs(gse)
str(Data)
gse
Data.class<-class(Data)
Data.class
attributes(Data)
Data.dim<-dim(Data)
Data.dim
Data<-Data[1:20,]
attributes(Data)
dim(Data)
str(Data)
heatmap(Data)
mock<-Data[,c(1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31)]
infected<-Data[,c(2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32)]
#t-test
infected.summary <- summary(infected)
infected.summary
mock.summary <- summary(mock)
mock.summary
mock.mean<-apply(mock,1,mean,na.rm=TRUE)
infected.mean<-apply(infected, 1,mean,na.rm=TRUE)
Data.test<-t.test(x=mock,y=infected,var.equal=TRUE)
Data.test
#boxplot_for_control_test
boxplot(mock, notch=F,varwidth=T,main="Mock boxplot", outline=TRUE,las=2,col="#8EEC9C")
boxplot(infected, notch=F,varwidth=T,main="Infected boxplot", outline=TRUE,las=2,col="#F08080")
m<-rep("1",16)
i<-rep("0",16)
GeneSamples<-paste(m,i,sep = "",collapse = "")
sml<-strsplit(GeneSamples,split = "")[[1]]#notice
gs<-factor(sml)
ord <- order(gs)
groups <- make.names(c("mock","infected"))
palette(c("#B580F5", "#33DAFF"))
# order samples by group
boxplot(Data[,ord], boxwex=0.6, notch=F, main="boxplot", outline=FALSE, las=2, col=gs[ord])
legend("topright",groups, fill=palette(), bty="n")
#scatterplot
pairs(~mock+infected,data = Data,main = "Scatterplot Matrix",pch=20,col="#FCBDBD")
#Mock_Infected scatterplot
plot(mock,infected,xlab = "infected",ylab = "mock",pch=20,col="#F1A78D"
     ,cex=1, main="Mock_Infected scatterplot" )