[BioC] Background analysis on

[james perkins]

Dear All,

I'm comparing 2 different, but similar tissue types (2 different parts 
of the nervous system), to work out the difference in expression between 
the two.

My question is this, when performing background adjustment and 
normalisation, should I split the tissue types and work on each one 
seperately, or should I normalise for all against all? The tissue type 
are quite similar and an MAplot / pairs plot of all the expression 
values at probe level (before any analysis) shows fairly similar 
distributions of intensities between the different tissues.

Many thanks,

Jim