[BioC] Comparing microarray data from different platforms

[Sean Davis]

On Thu, Oct 3, 2013 at 8:55 AM, Ahmet Sinan Yavuz
<asinanyavuz at 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