Some code additions to the script, in case you missed them:
This won't work as there was no first row labelled "Cd69" "Cd69" was an entry in row 1, but the first row name is simply "1"
mean(as.numeric(sup3["Cd69",2:15]))Instead, returns a vector saying which entry in column 1 is "Cd69" (All entries are FALSE, except first entry)
sup3[,1]=="Cd69"
mean(as.numeric(sup3[sup3[,1]=="Cd69",2:15]))We can change row names to be the gene names
rownames(sup3) <- sup3[,1]Plotting more than one column with boxplot
colnames(sup3)
boxplot(sup3[, c("MF.ctrl", "MF.LPS")])
hist(sup3[,"MF.ctrl"])
boxplot(sup3[ ,2:4])Histogram of CD3 values from the gvhd data
hist(gvhd[,5], xlab="CD3 values")
abline(v=280, col="red")