[BioC] limma and Volcano Plots

[Saket Choudhary]

I am working on a Proteomics microarray data using only the Red
Channel, though there are both R and G channels. The objective is find
DE genes in Grade2 samples of cancer as compared to Controls.

I created a gist here : https://gist.github.com/saketkc/8669586
Targets file: https://gist.github.com/saketkc/8669785
Volcano Plot: http://share.pho.to/4e1QT


I am a bit skeptical about the nature of my volcano plot, showing
quite high log odds and skewed. Have I, in the process of playing
around with the code, committed a mistake somewhere?



Saket