Hello,
   
  I  have four CHIP-on-chip datasets on affymetrix mouse promoter 1.0 R array, which are duplicate for both target protein and control group. By using makePlatformDesign and oligo packages, I have successfully read in the *.cel files. Now, I am stuck for the next step. Which package should I use for normalization and further statistic analysis? This is my first time dealing with CHIP-chip tiling array. Would anyone kindly help me out?
   
  Really appreciate your help!
   
  Yanqin  

       
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