This is a beginner question.
I have drawn up a box-plot and PCA plot for my RNA-seq experiment before and after normalization. However, I don't understand how to interpret the plots. For example, in the PCA plot, are the biological replicates expected to cluster by the first principal component? What about cluster on the second principal component? If I see my samples are clustered in a box-plot, does that mean my normalization has done the job?
What does a perfect normalization would look like on a box-plot and PCA plot? Any online resources?