Hi,

I am new in RNA-seq analysis via Deseq2. I want to study differential gene expression pattern in two different genotypes in two different time points with four treatments (including control) in each genotypes (3 replicates). Please suggest me the proper codes for the analyses. Models to be used: cultivar+time+cultivar:time, time+time:treatment

Thanks

# Notes:
# cultvar1= Resistance; cultivar2= Susceptible
#time1=5th day; time2=30th day
#Treatment= (4= SCN Only R; 5= Aphid Only R; 6= SCN+Aphid R, 7= COntrol R, 1= SCN Only S, 2= Aphid Only S, 3= SCN+Aphid S, 8= Control S)
cultivar <- as.factor (c(1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2))
time <- as.factor (c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2))
treatment <- as.factor (c(4,4,4,5,5,5,6,6,6,7,7,7,1,1,1,2,2,2,3,3,3,8,8,8,4,4,4,5,5,5,6,6,6,7,7,7,1,1,1,2,2,2,3,3,3,8,8,8))

cond <- data.frame(cultivar,time,treatment, stringsAsFactors=TRUE)

cond <- as.data.frame(cond)
sapply (cond, class) ##all should be factors

cond[,1] <- factor(cond[,1])
cond[,2] <- factor(cond[,2])
cond[,3] <- factor(cond[,3])

"Please suggest me the proper codes for the analyses"

This isn't exactly how the Bioconductor support site works. The goal is to provide software support, in particular beyond all of the documentation in the vignette and manual pages. You can see ?results for details on extracting contrasts after having run DESeq()

You might have a question about a particular comparison or contrast. It would be appropriate to attempt this after having read the help and examples in ?results, and then ask if this is the correct interpretation of the comparison or contrast you are interested in, but the developers do not write out all of the analysis code and its interpretation for you.