[BioC] limma and Volcano Plots

[Saket Choudhary]

Also, is there a more established way of dealing with Proteomics data
using limma?

On 28 January 2014 21:09, Saket Choudhary <saketkc at gmail.com> wrote:
> 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