Hello Ahmet, 
that is a interesting problem.
1 Use a common pool of probesets based unigeneID : package BioMart.
2.The QC: I think that provide a QC for Affy, and QC for illumina separately is OK: simpleAffy, and lumi package 
3. After you extract a raw data matrix composed of 2 experiment.
3.a you evaluate if the platform effect has a impact on the expression level compared to the condition effect: VEGAN package or rdatest(). The idea here is estimate what is the quantity of variance explained by the platform effect, and avoid that this variance biases your analysis.
3.b batch effect correction: Is it possible to remove the platform effect? that's the question 
3.c: redo 3.a  and compare the result: answer the question: the correction in 3.b is benefit?
4 The normalization : I have no really a good advise, but look in the literrature about that. May be, naively, I will applied a quantile normalisation.
5.The differential analysis could be classic, but include the effect platform would be pertinent. 

That's quickly what I think

Greg



________________________________
 De : Ahmet Sinan Yavuz <asinanyavuz@sabanciuniv.edu>
À : bioconductor@r-project.org 
Envoyé le : Jeudi 3 octobre 2013 13h55
Objet : [BioC] Comparing microarray data from different platforms


Hello,

We have 2 datasets, one from Illumina HumanHT-12 v4, and the other one is from Affymetrix Human Genome U133 Plus 2.0 Array. We would like to perform a differential gene expression analysis. What would you suggest in quality control, background correction and normalization steps in order to perform such analysis?

Thank you very much!

Ahmet Sinan Yavuz

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