A good place to start would be to look back to where limma was originally used, i.e., for microarray analyses and microarray normalisation, and i highly recommend Professor John Quackenbush's great paper on this: http://www.cs.cmu.edu/~zivbj/class05/reading/norm.pdf

Then I would read-up on linear modelling and linear regression, as limma is fundamentally based on linear modelling.

Finally, with that under your belt, I would read the actual work by the 'new' limma authors:

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402510/
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937821/

Part of being a great researcher is being able to read and understand your colleagues' published works, but I can understand that entering a new field can take time when there are literally 1000s of articles already out there on the topic.