Analyse RNA-seq differential expression data

Question

[guillaume.rbt]

Sorry in advance, I'm sure this question has already been posted before, but I haven't been able to find a satisfying answer.

I have to analyse RNA-seq differential expression data, and I've never done that before. So I have a big list of genes with different FDR and log fold change.

What is your method to extract relevant information from this? I've read that just putting arbitrary threshold is not a good solution, but I don't really know how to filter those results...

Any advice is more than welcome!

[Farbod]

Hi, You can check this, too:

https://groups.google.com/forum/#!searchin/trinityrnaseq-users/fdr|sort:relevance/trinityrnaseq-users/T9VBfIAMbjU/VPMoYWfpEQAJ

bonne chance!

Answer 1

[Benn]

FDR adjusted p-value < 0.05 is pretty standard. I am not a big fan of Fold change cutoffs, but a 1.5 or 2 fold change cutoff is often found in literature.