After normalizing the data with TMM method in edger one gets lots of values <1. Unfortunately, I found neither in edger manual nor in edger paper the description how the log fold change is calculated. Especially how those values <1 are treated because for instance, the log2 fold change of (0.7/0.03) is 4.544321 what is quite high log2 fold change but it resulted by dividing with a small number. How are the low normalized counts are treated when log2 fold change is calculated?
Give an minimum working example with code, because it's not clear what you're describing.