I have three different treatment times (0h (untreated), 3h and 6h), and three samples for each time point, 9 samples in total. I want to perform a single test to identify exons where the level of expression is dependent of the 'dose' of time; 0h<3h<6h OR 0h>3h>6h .
I have read the vignette, and know I have to set up the reducedModel and fullModel:
fullModel = ~ sample + exon + time:exon
reducedModel = ~ sample + exon
I am not sure I have this right. Would someone be able to suggest these model arguments please? I have no additional technical or biological covariates I need to correct for.