False discovery rate (FDR) Microarray

Question

[jaqy]

Hello,

Please can you advise me, what is the best false discovery rate (FDR) to select a list of activated genes (up or down regulated): FDR = 0.05 or FDR = 0.1?

Thank you in advance

[Jean-Karim Heriche]

You can think of the FDR as the expected proportion of false positives. So do you want your final gene list to have 5% false positives or 10% ? It usually depends on what you want to do with your list. Also if you plan on doing expensive follow up experiments on just a few genes, you might want to consider a more stringent multiple testing error correction method.

[jaqy]

thanks a lot Jean-Karim Heriche, your answer really helped me :)