Hi sorry I am totally new to data analysis and I see Log2 FC and Log2 Ratio often being used interchangeably, but they mean the same thing. I see Log2 FC more often used. However, is it more correct to use the term log2 ratio? Because to log2 transform FC data, it is not possible for negative FC values. Please correct me if I am wrong. Thank you for the clarification.
I am worried if your choice of word 'symmetric' brings more confusion to the discussion. It can be interpreted as the distribution of FC being symmetric on either side of 0, which is not the case as in differential expression expts, the up/down-regulated genes usually differ in not only numbers, but also in range of FC. Probably something like 'uniform scaling' will be a better choice
I think Damian's explanation makes sense. The second paragraph reads well and was clear to me. The only thing i'd add is that you don't have to log2() to get a symmetric-around-0 score - any logarithm will do. Actually i have no idea why we use log2 and not log10 or logn.... does anyone know?
Understanding up and down regulated genes from LOG2 foldchange or foldchange
Ah, i see - it seems like it's really only for historical reasons then. The first link gives an example that when the change is 2 fold, then number is '1' which is easy to see when things double.... however that's kind of a cheat because it doesn't really work for any other number. tripling for example gives you the not-so-nice value of 1.584962500721156 :P
To be honest, for my personal use I tend to prefer other calculations anyway. log() is an expensive way to get a ratio that doesn't work with negative values -_-;
Great explanation Damian, I appreciate it!