sidebysideANOVAboxplots.R

#read macaque data
setwd("/home/rosseraa/work.dir/allen.brain/")
macaque.raw.data = read.csv("macaque.common.regions.ANOVA.csv")

#standardize (z-score) macaque expression values
macaque.raw.data$expression = scale(macaque.raw.data$expression)

#run macaque ANOVA
aov.result = aov(expression ~ region, data=macaque.raw.data)
summary(aov.result) #is there a significant difference between any of the group means? If so, move onto a post-hoc test
TukeyHSD(aov.result) #post-hoc for multiple pairwise comparisons to see significant differences
summary(aov.result)[[1]][["Pr(>F)"]] #p-values
print(model.tables(aov.result, "means"), digits=4)

#read human data
human.raw.data = read.csv("human.common.regions.ANOVA.csv")

#run human ANOVA
aov.result = aov(expression ~ region, data=human.raw.data)
summary(aov.result)
TukeyHSD(aov.result) 
summary(aov.result)[[1]][["Pr(>F)"]] #p-values
print(model.tables(aov.result, "means"), digits=4)

#visualize
par(mfrow=c(1,2))
boxplot(expression ~ region, data=macaque.raw.data, pch=20, main="macaque", las=2)
boxplot(expression ~ region, data=human.raw.data, pch=20, main="human", las=2)