I have 2 RNA sequencing datasets and would like to compare their raw read counts.
cor(log(data$set1), log(data$set2)) 0.8734045 cor(data$set1, data$set2) 0.2376726
I have tried to plot them (raw read count and log transformed). I have attached pictures. The log transformed plot look weird. Did I run it correctly?
plot(log(data$set1), log(data$set2)) plot(data$set1, data$set2)
Can I improve the plot? Thank you for you suggestions! log