Possibly this is a trivial question, I'm missing something:
My experiment is based on the model
~ pos + ring + pos:ring
the factors can take the following values:
pos = {Base,Junction,Tip}
ring = {Down,Up,Top}
I made two DESeq2 runs, where in the first run I used the default levels of factors (as above),and in the second run I releveled the order of ring to {Up,Down,Top}. When testing the effect of "pos_Junction_vs_Base"
, I got 7 and 915 signifcant genes in run1 and run2, respectively. So, if my interpretation is correct then at ring=Down only 7 genes differ between Junction and Base, compared to 915 at ring=Up.
If the above is correct then I expect that the interactions "posJunction.ringDown"
and "posJunction.ringUp"
will give about 900 signifcant genes each, to reflect the difference in Junction vs Base response between ring=Down and ring=Up. But I see only 3 signifcant genes for these interactions.
thanks a lot for any help !
Just make it easier for people to help you. Write out explicitly how everything is leveled at each step, every design command line, and every results call.