Hello all!

I have a basic conceptual question:

I have a set of RMA normalized data that I am looking to carry out  
hierarchical clustering.
In the past we've usually been working with MAS5 data which we import  
into dCHIP to carry out the clustering.
I'm now looking to do the same with RMA data, and I'm wondering if I  
should transform to a linear scale or leave it the typical log2 scale.
dChip does a per gene normalization (subtracts the mean and then  
divides by the standard deviation), and it appears that linear or log2  
scale affects the results.

I'm assuming most people just leave it log2 scale, am I overthinking  
the whole issue?

Thanks,


_________________________
Ryan Kirkbride
Plant Biology Graduate Student
Harada Lab
UC Davis





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