Hi all,
 
I'm dealing with a number of human lymphoma samples, some of which have
been in freezer storage for up to 20 years. The samples have been run on
HGU133Aplus2 chips, and have a wide range of 5' to 3' slopes (as
determined by the RNAdeg function), ranging from 3.8 to 9.5.
 
My understanding is that normalizing chips with such a wide range of
slopes could lead to innacuracies downstream.
 
1) Are these slopes too different to allow for the chips to be
normalized together?
 
2) if not, how would one go about working around these slope
differences? Our PI is dead set on extracting any info possible from
these 'rare' samples.
 
many thanks
 
Tarun Nayar
Genome Sciences Centre
Vancouver, BC

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