[BioC] different density

[Jakub Mieczkowski]

Hi All,
I'm new to Bioconductor and I want to analyse time course data (6 time
points, 3 oligo arrays in each). During the quality control (QCReport) I
found that 4 arrays have different densities. What is shown here:

http://students.mimuw.edu.pl/~jm214641/BoxANDden.pdf

Plot of NUSE shows differences too. Images of weights are a little bit 
different form rest, but I can't notice any artefacts.
3 of them, are from the same time point.

Should I remove them from further analysis (differences can have 
biological basis)? Or maybe I just can't use methods like RMA (because 
of different distributions)? Do you have any suggestions?
Thanks,
Kuba