I carried out RNA-seq for WT strain and a mutant strain of gene X, grown under two conditions (no treatment, treatment). To extract the effect of gene X on changes in gene expression between treatment and no treatment, I applied DEseq2 with the "interaction" option.
My design :
~genotype + condition+ genotype:condition
For quite a few genes I got substantial log2FC values for the interaction term but the padj values are NA.
For the same genes the individual comparisons yielded statistically significant results [e.g. WT(treatment vs. no treatment) and treatment( WT vs. mutant of gene X).
Here are two examples, one with statistically significant padj for the interaction, and another one with NA. Numbers are for log2FC and padj
Gene Basemean Treatment (WT vs mutant) WT (treatment vs no treatment) No treatment (WT vs mutant) Mutant (treatment vs no treatment)Interaction Gene A 2201 -3.96, 0.000 -4.13, 0.000 -0.57, 0.769 -0.743, 0.145 -3.387, 0.000 Gene B 65.523 -3.310, 0.001 -3.250, 0.002 0.101, 0.993 0.161, 0.911 -3.411, NA
I believe I can conclude that gene X has an effect on the expression change of gene A between treatment and no treatment. What would be the conclusion for gene B, which has a substantial log2FC for the interaction but the padj is NA? Of note, it is clear that without an active gene X there is no change in gene B expression between treatment and no treatment (log2FC of 0.161).