Hello Sir,. I have a transcriptome data with three conditions uninfected, mock and infected(x,y,z)for thre genotypes suppose (A,B,C) and three time point conditions (0day,2day,4day) . Which model should i put for these three so that i can see the interaction . The problem i am facing is that my uninfected (0 day samples) are less than that 2 day and 4 day . If i have 45 samples -: Sample Genotype condition time
C01 CIBC-5 uninfected 0dpi
C02 CIBC-5 uninfected 0dpi
C03 CIBC-5 uninfected 0dpi
C21 CIBC-5 infected 2dpi
C22 CIBC-5 infected 2dpi
C23 CIBC-5 infected 2dpi C41 CIBC-5 infetced 4dpi C42 CIBC-5 infected 4dpi C43 CIBC-5 infected 4dpi E01 Ei-2 uninfected 0dpi
E02 Ei-2 uninfected 0dpi
E03 Ei-2 uninfected 0dpi E21 Ei-2 infected 2dpi
E22 Ei-2 infected 2dpi
E23 Ei-2 infected 2dpi E41 Ei-2 infected 4dpi
E42 Ei-2 infected 4dpi
E43 Ei-2 infected 4dpi
Z01 Zdr uninfected 0dpi
Z02 Zdr uninfected 0dpi
Z03 Zdr uninfected 0dpi
Z21 Zdr infected 2dpi
Z22 Zdr infected 2dpi
Z23 Zdr infected 2dpi Z41 Zdr infected 4dpi
Z42 Zdr infected 4dpi
Z4_3 Zdr infected 4dpi

This is a complex experimental design, and I'd recommend you work with a local statistician to help you determine your biological questions of interest and to formulate these into a linear model, and help you to interpret results.