Hi. I have some doubts about statistics of DGE analysis (RNAseq data).
- Some packages use the likelihood ratio test (LRT) and other use quasi-likelihood (QL) F-test. What is better and why? Can I use qlFtest if I have replicates?
Please, share with me all the bibliography references to understand it.
- I have the following experiment: Two populations (North and South) and in each population, I have my conditions (3 Host Plants). Each Population x HostPlant 'subgroup' has two biological replicates, giving a total of 12 samples (two replicates for each population x host plant).
My interest is determinate the DGE between host plants, but I wondering if the population has and effect in DGE. We are thinking of doing a two-way ANOVA to test the effect of the two factors, but I'm not sure if it is the right approach.
My question is, Is it correct to do a two-way ANOVA? How could I do it? I read some blogs to DEseq and edgeR with analysis like ANOVA, but I'm not sure to understand it. I think that my model could be: ~population+hostplant and using models to batch effects. Again, if you have bibliography references, please share it with me.
Thanks you so much for your help Sandra
I removed the DESeq2 tag, as it seems like you are interested in using edgeR here from reading over your question. Note that when you add a package tag it directly emails the developers.