Hi there, I'm new to this analysis area, and I already look into many threads, but still don't understand the meaning of "mean normalized counts" in MA plot. Is it the mean normalized read counts between comparison groups? If so, what's the biological meaning of it, and also with fold change ? Thanks!
It indicates the average expression between the groups you compared, which is simply the mean of the normalized counts of the samples used in the comparison group. The "meaning" is that genes with higher counts are more trustworthy (=have higher statistical power) than low count genes. Biologically this is because either the gene is lowly expressed and/or short and therefore intrinsically gets lower counts than a longer one at equal expression level.

