Dear DESeq2 developer and colleagues,
DESeq2 generates an output table including "log2FoldChange". I have two questions about this value.
I. As far as I know, this is a moderated version, not a log2 fold change from the raw count value. But I want to have unmoderated value that can be calculated from count directly and my current way is: (1) get normalized count (2) log transformation (3) calculate averages per condition (4) divide two averages: "FC". Is this a right way? I am confusing whether it is fold change of log, or log of fold change.
II. Effect size is "log2FoldChange" divided by SD where SD is sqrt(1/mu + dispersion). Here, I think that mu is an average of "log" of normalized count and dispersion can be retrieved by a command "dispersions()". I assume that this command outputs in a same order with "results()" to match values between two output objects. Also, I can use moderated version or unmoderated version with the same formula, mu and dispersion. Are they correct ?