I am hoping to receive some guidance on a longitudinal RNA-sequencing project I've conducted. I have sequences at multiple ages across 3 different disease models in addition to control. I am running a likelihood ratio test in DESeq2 with the full and reduced models as specified:
full: ~ genotype + age reduced: ~ age
I realize that I am testing for the effect of genotype, controlling for age, one gene expression with this test. However, I'm unsure how to interpret the DESeq results and particularly the log fold change result. The padj values are simply telling me whether my full model is a better model to capture deviance of gene expression, without taking into account log2fold change differences. Does this mean I could have significant DEGs for which the log fold change in expression is actually 0?