I am analysing RNA-seq data of two genotypes (A and B) in order to detect the transcripts that are involved in a physiologic change that takes place earlier in genotype A and later in genotype B. For genotype A there are 2 time points (A0 and A1) and for genotype B there are 3 time points (B0, B1 and B2), with 3 replicates each (15 samples in total). The reason for not having A on time 2 is that by time 1 such physiologic change has already been produced. (The change has already been produced on A1 and on B2.)
I performed abundance estimation using RSEM and I want to perform differential expression analysis using limma. I am not sure this can be considered a time course experiment as I only have 2 samples for genotype A and I don't have the same number of time points for both genotypes. My idea is to select the transcripts that are differentially expressed between A and B on time 1 (A1-B1) and the transcripts that are not differentially expressed between A1 and B2. However, selecting the transcripts which are significantly not differentially expressed is complicated, since transcripts not appearing in the list of differentially expressed are not necessarily not-DE.
Is there a way that to write my contrast matrix in order to find the transcripts I am interested in?
Thank you for your attention.