What is the exact number of gene that we can detect from differentially expressed gene?

Question

[Angela]

Hello, I did differential expresses gene by using DESeq2 between 18 cancer sample and 4 control sample, and I found 6753 by alpha 0.05. could you please explain me it is a real number of differentially expressed gene or not? Have I change some statistical threshold in analysis to do better? Thanks in advance

Answer 1

[Antonio R. Franco]

You need to apply a filter, and everyone has their favorite In my case, I use a filter of a Lof2FoldChange >= 1 or 2, and a p-adj value <= 0.05 or 0.01

[Angela]

thank you Antonio,

I changed the threshold of log fold change to 1 and also 2, with p-adj value <= 0.05 and I found less than 1000 expressed gene!!! that's strange could you please guide me more?

Answer 2

[JC]

Cancer is highly variable, even tumours from the same patient are different, you can see this in a PCA or similar plot. So it's not surprising that you get 6k DEG, beside FC, you can also filter by the number of samples sharing the gene as DEG, like filtering by genes as DE in 50% of your samples.

[Angela]

thank you JC

I'm new in differential expressed gene, could you please guide me more about filtering by genes?