This is a basic question, I hope you do not mind, why there are negative values in v$E, after voom tranformation. I have not understood

Code should be placed in three backticks as shown below

Suppose that a gene has a counts-per-million value of CPM = 0.5. What do you think log2(CPM) would be?

It's completely normal to have negative log2CPM values. You might perhaps be confusing expression and log-expression. Expression values are always non-negative but log-expression can be positive or negative. That's routine and doesn't pose any problems. It's just the nature of logarithms.