Hi

check fRMA package (frozen RMA) and relevant publication
http://www.bioconductor.org/packages/2.12/bioc/html/frma.html

good luck
Alyaa


On Thu, Oct 3, 2013 at 4:03 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Thu, Oct 3, 2013 at 8:55 AM, Ahmet Sinan Yavuz
> <asinanyavuz@sabanciuniv.edu> wrote:
> > 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?
> >
>
> Hi, Ahmet.
>
> What is the experimental design?  In other words, what do you want to
> compare for differential expression?  What is the layout of samples on
> the two array platforms?
>
> These questions are important to answer, as if you are comparing two
> groups, group A and group B and all the group A samples are on Affy
> and all of group B are on Illumina, I do not think you are likely to
> be able to perform your analysis directly.  If samples from groups A
> and B are both represented on both platforms, you may be able to move
> forward.
>
> Sean
>
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-- 
Alyaa Mahmoud

"Love all, trust a few, do wrong to none"- Shakespeare

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