Question: Interaction term for condition, time point and genotypes together in DESeq2
0
7 months ago by
hamsasekar020 wrote:

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
C0
2 CIBC-5 uninfected 0dpi
C03 CIBC-5 uninfected 0dpi
C2
1 CIBC-5 infected 2dpi
C22 CIBC-5 infected 2dpi
C2
3 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
E0
3 Ei-2 uninfected 0dpi E21 Ei-2 infected 2dpi
E2
2 Ei-2 infected 2dpi
E23 Ei-2 infected 2dpi E41 Ei-2 infected 4dpi
E42 Ei-2 infected 4dpi
E4
3 Ei-2 infected 4dpi
Z01 Zdr uninfected 0dpi
Z0
2 Zdr uninfected 0dpi
Z03 Zdr uninfected 0dpi
Z2
1 Zdr infected 2dpi
Z22 Zdr infected 2dpi
Z2
3 Zdr infected 2dpi Z41 Zdr infected 4dpi
Z4
2 Zdr infected 4dpi
Z4_3 Zdr infected 4dpi

deseq2 • 121 views
modified 7 months ago by Michael Love25k • written 7 months ago by hamsasekar020
Answer: Interaction term for condition, time point and genotypes together in DESeq2
0
7 months ago by
Michael Love25k
United States
Michael Love25k wrote:

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.