Hello,



I have a question about background correction and normalization. Please help me out! Thank you for your time!



I have four chips of microarray experiments, and therefore four data sets. I combined them together by merging on ProbeID and read in them as one file using read.ilmn(), and I combined all the control probe files into one and read it in. I just followed the limma user guide and use neqc() for background correction and normalization. Is it good enough? Do I need to consider within array and between array normalization?



Thanks,
Xiayu

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