Plotting Exercise 3

These exercises cover the sections on Plotting in R PlottingInR.

Section 1 - volcano plot

• Use the example from the course ("../data/DiffEx.csv"), and

  • use padj < 0.01 and abs(log2FC) > 1 as thresholds to define DE genes

  • change the colour codes for the volcano plot to c("Up.DE","Down.DE","non.DE") = c("#B2182B","#2166AC","grey") and generate the volcano plot below

  • show the GeneSym for the top 10 DE genes based on padj

• hints:

  • use read.csv() to import DiffEx.csv to R

  • if you failed to import DiffEx.csv to R, please check whether you set up your work directory properly by using getwd() and setwd()

Section 2 - MA plot

• MA plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log FC ratio) and A (mean average) scales, then plotting these values

• Please use columns 'log2FoldChange' and 'log2(baseMean)' to create the MA plot