[BioC] nimblegen ChIP to chip array

[Simon Knott]

Hello Dr. Tamir

I'm working with nimblegen tiling arrays and I am dealing with some  
normalization issues. In looking into the problem, I noticed a thread  
on the bioconductor message board where you stated that after some  
tests and discussion, you advise against loess normalization when  
using these arrays. I too have noticed some problems (via the  
MAPlots) when I used Loess normalization. Qualitatively I'd say that  
my data looks better and more reproducible when I only use the  
Nimblegen normalization. Could you elaborate on the issues that  
you've noticed when using loess on the nimblegen arrays??

Best Regards

Simon Knott
PHD Student
University of Southern California
Department of Computational and Molecular Biology