Hi,

I am analyzing a data where I have 10 samples (5 control and 5 disease) and each sample has 2 replicate. The data for RNA-seq is generated for 0 and 12 hours for Brain and Lungs. I used DESeq to identify differentially expressed genes in Brain vs Lung for 0 and 12 hours. But I also want to identify DE genes at 0 and 12h in brain and 0 and 12h in Lungs.

I was thinking of using ANOVA as my matrix looks like something like this for each gene and for each replicate.

              0          12

Brain    EB0      EB12   

Lung    EL0       EL12 

ANOVA will give me p-values within sample and across sample for each gene.

Another problem is that I have more variables control and treatment. Ultimately I want to find DE genes between control and treatment also.

Its a messed up complex data and any help or referral to paper is highly appreciated.

Thanks for consideration.