Hello, John,
 
I read your post on BioC mialing list and I don't have an account
there.  So I have similar problem to process agilent 244k arrays.  And
after check the code, I found that readPositionInfo() has something
missing: the Position information.  So what I have done to fix the
problem is as follows:
 
RG2$genes$Position = (RG2$genes$Start + RG2$genes$End)/2
 
before backgroundCorrection.
 
Hope it helps.
 
Best Regards,
 
Jianmin Wang


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