I was referring to edgeR user guide example 3.3.1 to analyze my data which has 2 condition, 2time points and 3 genotypes,and that look like,
Treat Time Genotype Sample1 Control 0h G 1 Sample2 Control 0h G 1 Sample3 Control 1h G 1 Sample4 Control 1h G 1 Sample5 Control 0h G 2 Sample6 Control 0h G 2 Sample7 Control 1h G 2 Sample8 Control 1h G 2 Sample9 Control 0h G 3 Sample10 Control 0h G 3 Sample11 Control 1h G 3 Sample12 Control 1h G 3 Sample13 Stress 0h G 1 Sample14 Stress 0h G 1 Sample15 Stress 1h G 1 Sample16 Stress 1h G 1 Sample17 Stress 0h G 2 Sample18 Stress 0h G 2 Sample19 Stress 1h G 2 Sample20 Stress 1h G 2 Sample21 Stress 0h G 3 Sample22 Stress 0h G 3 Sample23 Stress 1h G 3 Sample24 Stress 1h G 3
As additional factor "Genotype" is included, I am not sure how to make groups and contrast. I was thinking like treatment time for each treatment condition for each genotype is a group,
Group <- factor(paste(targets$Treat,targets$Time,targets$Genotype,sep="."))
In this case, how can I make contrast for identifying genes for ex,that are induced at 1hr drug treatment for only genotype "G 2"?