Hi I have noticed while comparing kooperberg background correction with normal background correction that on my M vs A plots, the kooperberg method seems to have a LOT more negative M values at low A values than the normal background correction method - in fact, it makes the M vs A plots look more like "hump backs" than the traditional "nike swoosh" (if anyone can tell what I am talking about!) Can anyone think why kooperberg might create more negative log ratios?? I realise that most of the effect of kooperberg will be at the low-A end of the spectrum, but why would it necessarily create more negative ratios than postive ratios? Perhaps my negative values are only in one channel....?? Thanks Mick