Question: Cross-platform of microarray or analysis separately
gravatar for Morteza Hadizadeh
4 weeks ago by
Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
Morteza Hadizadeh20 wrote:

Dear all,

I want to find common genes for 4 different diseases, I have 4 microarray datasets with the same platforms (Affymetrix). Which is the best way for the determination of common genes? I merge all datasets and remove batch effects or analysis each dataset individually and then detect common genes?

I would be very pleased if you could guide me.

R gene • 115 views
ADD COMMENTlink written 4 weeks ago by Morteza Hadizadeh20

You can only remove batch effects if you have replicates of the samples in each batch (so each study) which you don't if I get this right. Therefore option two is what you should do, followed by some kind of meta-analysis.

ADD REPLYlink written 4 weeks ago by ATpoint40k

The second option is more robust here. you can undertake a ranked-based meta-analysis approach like This package do was intorduced to resolve similar issues.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Hamid Ghaedi500
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