First I just want to say, I know this has been asked numerous times and in a number of places. However my confusion has increased progressively!
If someone could set the record straight, please, on how to generate a TMM normalized counts using EdgeR, I would be incredibly grateful!
This post has two answers that look like disagree with one another... output TMM normalized counts with edgeR
The main reason I want to generate TMM matrix from my count matrix is to compare gene expression levels within samples (see the level of multiple cell-type markers within a single sample) in a bar plot, and then generate the same bar plot for every other respective sample to compare between samples.
I think using TMM normalized counts will allow me to compare between samples and within samples according to here: https://hbctraining.github.io/Training-modules/planning_successful_rnaseq/lessons/sample_level_QC.html
I plan to use something like this to generate the bar plots: Network/Pathway Analysis from Mass Spec data
Any help would be appreciated.
Thank you in advance :)