macaque.ANOVA.R

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

#standardize expression values
raw.data$expression = scale(raw.data$expression)

#run ANOVA
aov.result = aov(expression ~ region, data=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 where the significant differences lie.
summary(aov.result)[[1]][["Pr(>F)"]] #p-values
print(model.tables(aov.result, "means"), digits=4)
boxplot(expression ~ region, data=raw.data, pch=20)