Gordon K Smyth | 28 Jun 09:37 2013
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read.ilmn() and variation between chips

Dear Xiayu,

Yes, it is good enough.  neqc() has done between-array normalization 
already, and there is no need for within-array normalization for Illumina 
BeadChips.

Please look at the help page

   ?neqc

The read stages that you describe sound complicated.  read.ilmn() reads 
the files as output by Genome Studio at our core facility without any need 
for intermediate processing.

Best wishes
Gordon

-------------------- original message --------------------
[BioC] read.ilmn() and variation between chips
Rao,Xiayu XRao at mdanderson.org
Wed Jun 26 20:08:09 CEST 2013

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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