[BioC] right normalization?

[andrea.grilli at ior.it]

Hi list,
I've got 16 gene chip affymetrix arrays of 2 cell lines at different
time/conditions. Chips were done in 2 different moments, and this bias
seems to affect my analysis.

I've normalized with RMA and analyzed with eBayes models to compare
the 2 cell lines at each time point.
Following analysis are affected by the above mentioned "time bias",
like in clustering were data are grouped according to when the arrays
were hybridized.

- Do you suggest a different normalization? Which one could reduce
this effect?

- could be a good approach normalizing the 2 groups of samples
separately (will be 8 and 8) and merging the data after normalization?


I did quality control steps like in bioconductor book, and all
parameters are in the right ranges. Also box plot shows a similar
expression range across samples.
Any help will be really appreciated,
thanks in advance,

Andrea



PS This is a semplification of a previous mail, sorry for the repetition.