With the Life Module system, the negative and positive qualities you get are calculated with the normal 1x karma for 1x karma. And it still says the 25 point limits of positive and negative qualities are still in effect, but if a life module gets you more negative than 25, then you have to buy back your negative qualities to under 25 if you want to swap them around. Similar but inverse for positive qualities.
I'm trying to make a character with Life Mod and I have a ton of negative qualities, all which I'm going to keep because they're awesome and help flavor up my street sam.