[BioC] Double-logging in lumi + loess?

[Michal Blazejczyk]

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