Hi again, I've been reading the code of lumiN() function... If I call it with method = 'loess' then lumiN() will call normalize.loess() to normalize the data. However, normalize.loess() has a parameter called log.it which defaults to TRUE. Doesn't it mean that if I stabilized my variance prior to calling lumiN(), and then call lumiN() with method = 'loess', my data will be double-logged? I know that I could simply provide log.it = FALSE when I call lumiN() but this looks like a potential problem for users who won't attentively read the whole documentation. Best, Michal Blazejczyk