Three design matches to model GLM as in edgeR manual page 32.

This is a simple data visualisation to know the differences. The data is TMM normalised and plot is made. I did this to see how the dispersion estimation and GLM modelling is impacting particular genes which have large mean differences.

RNA seq data raw counts

Normalisation strategies for Differential gene expression including both theoretical and code for TMM, TMMwsp, RLE and UQ algorithms

Here I have am looking how number of differentially expressed genes varies by creating different data frames.