I would just like to point something out from my own experience considering healing and negative energies. This is a learn from my mistakes thing.
I am a 3rd degree Usui Reiki Master thingy (I hate titles), but when I reached 2nd degree I started to intuitively pull negative energy out of people. I don’t recommend it for your own sake, apparently not everyone can handle it. However, that’s the not the point of the story. One day I was doing a session with a guy I worked with. I decided to pull all of the negative energy out of his body because the general idea was, if there’s no negative energy then there won’t be any illness or dis-ease. So, that’s what I did, he felt absolutely fantastic and left to go home. The next day at work he came to me and told me he won’t be coming for any more sessions. He told me 2 hours after he left he literally didn’t have enough strength in his body to stand up. It took him the entire night to regain his strength.
My Reiki teacher decided to try and help me with this, and I did a session on her so she could ascertain the problem. Every little cut, scar or wound on her body became so infected, even a mosquito bite on her ear, that she ended up going to hospital. It was not a pretty sight. Anyway, she was a good teacher, and after she recovered, we continued. All I had to do was find a balance.
So the moral of the story is, leave enough negative energy to maintain a balance. Regarding your actual question, don’t transmute the negative energy, just add positive. What you are probably looking at is a lack of positive energy and so adding it will bring back the equilibrium.