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!
You could try averaging signal among probes for the same gene, consider only genes covered on both arrays, and then use quantile normalization to try and make them look the same.
However, I honestly wouldn't put very much trust in those results. I would strongly recommend looking for a leukemia cell line sample using an Affy array, so the probes at least measure the same thing. For starters, the NCI-60 cell lines are in a lot of GEO datasets, and I'm sure you can find other leukemia Affy datasets as well:
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
What is the comparison that you want to do for differential expression? What groups are represented on which array platform?
It was one cell line (A leukemia cell line) in illumina and one cell line (Mesenchymal Stem Cells) in affy.
Unfortunately, you are probably stuck since the effects of platform are perfectly confounded with the biological effect of interest.