I am currently trying to figure out this question. I have tried different keywords but I do not seem to find the right thread.
What I want to know is:
- Does limma arrives to a pvalue by using the log2 scale of the normalized array data?
- Does limma arrives to a pvalue using the normalized array data directly and then shows the differences as log2 fold changes in the top table?
If you know the proper thered to refer to, that will be of great help, else, I am grateful for your responses.