[BioC] nimblegen ChIP to chip array

[ping_zheng@mail.wsu.edu]

I have never analyzed microarray data, I would like to use Biochonductor 
to analyze data provided by nimblegen. Method used was ChIP to chip array 
and data is provided in the following format

*_ratio.gff, *_pair.txt, *_report.tab

How can I use normalizeBetweenArrays or Loess function for the data 
provided by nimblegen in the format specified above?
Can someone tell me what type of data is required for applying these 
functions?
Does the data format vary from company to company like nimblegen and 
affymetrix?

Thank you for your time and help


Ping Zheng