I conducted multiple pairwise comparisons between treatments using EdgeR and TMM method on ExpressAnalyst, and the only values that seem to change in my results are the log2FC. For example, when I run two different treatments in comparison with a same control group, I get exactly the same logCPM values for a given transcript (see images below). What do these values mean if they stay consistent for a given transcript?
Here is my bulk RNA-seq dataset with metadata included:
top_counts_cleaned_without_outliers.csv (2.2 MB)