  Hello:
   
  I am currently trying to understand the effect of background subtraction on gene expression in affymetrx genechip arrays. It will be really helpful if someone could let me know 
   
  "How to extract the PM and MM intensities along with their locations/coordinates on the chip after background correction?"
   
  I am enclosing a part of the code (my first try):
   
  library(affy)
  Data <- ReadAffy("File1.CEL")
  %then I load the corresponding CDF files
  eset <- mas5(Data, normalize = FALSE);
   
  Now I have the background corrected values in "eset". How can I get the PM and MM intensities along with their coordinates from eset.
   
  Thanks
   
   
   
   
   
   
   
   
   


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