I am currently working on an experiment and have some trouble with the design. I've looked on the bioconductor help pages and the manual, but I have the feeling that I am overlooking something simple. Maybe you could help with some insights, or point me to a post with a similar setup.
My setup is as follows:
genotype timepoint flexible GT1 T1 flex GT3 T1 flex GT2 T1 non_flex GT4 T1 non_flex GT5 T1 non_flex GT1 T2 flex GT3 T2 flex GT2 T2 non_flex GT4 T2 non_flex GT5 T2 non_flex GT1 T3 flex GT3 T3 flex GT2 T3 non_flex GT4 T3 non_flex GT5 T3 non_flex
I have 5 different genotypes (GT1..GT5) which are genotypically different. Each of these genotypes have been put in the cooler at T2 and after some time RNA was extracted. Later, the samples were put out cooler and after some time RNA was extracted (T3). Every genotype is either flexible or non-flexible (i.e. flexible means in this case they deal better with cold). For each of the sample/timepoint I have three biological replicates (omitted from the scheme above).
With this experiment I want to know which genes change over the different time points and what the difference is between genotypes while taking in account the flexible trait.
What I could do is making a design like this (which follows the example of the time series experiment found in the manual):
~ genotype + timepoint + genotype:timepoint
In which the genotype is modelled with the interaction over time. However in this case I don't take in account the flexible trait. With a result-set like that, I could easily calculate the overlap between between different interaction terms manually (i.e. (GT1T2/GT1T1) vs (GT2T2 /GT2T1)), but this doesn't seem the best way to go.
What I also could do is is replacing
flexible in the formula, which would make the design simpler but it will not take in account the differences between genotype, which is something I don't want. Do you have any tips to solve this?