Hello,

I have a RNAseq experiment where I have 2 conditions and 3 replicates each and replicates are taken from different individuals. So my design is as follows:

Sample Condition Individual
S1 treated A
S2 untreated A
S3 treated B
S4 untreated B
S5 treated C
S6 untreated C 

Here is my code to analyse the data using deseq2:

library('DESeq2')
directory<-"counts"
sampleFilesN1_N2 <- grep("*N[1-2]",list.files(directory),value=TRUE)
sampleConditionN1_N2<-c("treated","untreated","treated","untreated","treated","untreated")
sampleIndividual<-c("A","A","B","B","C","C")
sampleTable1<-data.frame(sampleName=sampleFilesN1_N2, fileName=sampleFilesN1_N2, condition=sampleConditionN1_N2, individual=sampleIndividual)
ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable1, directory = directory,design= ~ condition + individual)
ddsHTSeq$condition <- relevel(ddsHTSeq$condition, "untreated")
dds<-DESeq(ddsHTSeq)
res<-results(dds)
res<-res[order(res$padj),]
write.csv(as.data.frame(res),file="DeSEQ2_treated_vs_untreated.csv")

From help(results), I understand if I want to get comparison of conditions considering the pairing of samples into account, I should give 

res <- results(dds, contrast=c("condition","treated","untreated"))

Is this correct? 

Also is my design correct: design=~condition+individual?

Any help is hugely appreciated. 

Thanks in advance.