I am trying to visualize the gene expression difference between different samples. I am using edgeR to analyze rna-seq data. I have done PCA and MDS plots on the samples and the samples separate nicely into groups between treatments and time points. Now I would like to see how the genes separate on the same plot between samples. I would for example like to see if genes cluster with certain samples. I manage to create the PC plot with the help of prcomp() and use ggplot to visualize the data. Someone knows how I can do this?
Question: How to visualize gene difference with PCA?
2.3 years ago by
carl.h • 10
carl.h • 10 wrote:
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