Hi, I am a RNA-seq beginner. Recently, I have a RNA-seq project. There is one factor with 3 levels (A, B, C). Level A is tumor (9 biological replicates); B is tumor + treatment (8 replicates); C is control (6 replicates). I want to compare:
tumor vs tumor+treatment (I know how to do this) tumor vs control (I know how to do this)
Then I want to compare the overlaps of the the above: A+C vs B+C.
samples <- data.frame(row.names=colnames(countMatrix), treatment=as.factor(rep(c("A","B","C"),c(9,8,6))), condition=as.factor(rep(c("AB","AB","C"),c(9,8,6)))) colData<-pData(data)[,c("treatment","condition")] countData<-counts(data) dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~treatment+condition) dds$treatment <- relevel(dds$treatment, ref="C") dds<-DESeq(dds)