Hi all,
I am trying to run some RNA-Seq analysis using edgeR and am trying to visualize my results. When should I use plotMD(), maPlot(), or plotSmear()?
My understanding is that plotSmear() is an extension of maPlot() for DGEList input instead of two separate vector counts. The documentation says that plotSmear() is for "smearing of points with very low counts, especially those that are zero for one of the columns" while plotMD() is for "Creates a mean-difference plot (aka MA plot) with color coding for highlighted points." However, when I apply the two functions to my dataset my graphs look similar besides the color-coding in plotMD().
What is the difference between these functions and when should I use one over the other?
Thank you so much!