infile3= "bde.counts.transcriptome.csv"

countdata3<-read.delim(infile3, sep=",", header=TRUE, row.names=1)
head(countdata3)

#Separately define pieces:
sel.line <- factor(c(rep("GroupB",11),rep("GroupD",12), rep ("GroupE", 12)))

block <- factor(c(rep("1", 3), rep("2", 3), rep("3", 3), rep("4", 2),
                  rep("1", 3), rep("2", 3), rep("3", 3), rep("4", 3),
                  rep("1", 3), rep("2", 3), rep("3", 3), rep("4", 3)))
                   
ExpDesign3 <- data.frame(
  row.names = colnames(countdata3), 
  sel.line = sel.line,
  block = block) 

head(ExpDesign3)
  
CDS3 <- DESeqDataSetFromMatrix(countData = countdata3, colData=ExpDesign3, design= ~ sel.line + sel.line:block)
CDS3_1 <- DESeq(CDS3)
res3 <- results(CDS3_1)