Hi Rory,

I am trying to analyze my chipseq data of H3K4me3 with 4 conditions and 2 replicates. I have only 1 replicate for input.

I think I create the sample sheet correctly and it works until some points but in dba.analyze part I get error as following.

H3K4me3_narrow <- read.csv("chipseq_rep1_rep2.csv")
H3K4me3_narrow <- dba(sampleSheet = "chipseq_rep1_rep2.csv")
plot(H3K4me3_narrow)

H3K4me3_narrow<-dba.count(H3K4me3_narrow, minOverlap = 2)

plot(H3K4me3_narrow)   ####  error massage: "Error in .External.graphics(C_layout, num.rows, num.cols, mat, as.integer(num.figures),  :
  invalid graphics state"

H3K4me3_narrow<- dba.contrast(H3K4me3_narrow, categories = DBA_CONDITION)
H3K4me3_narrow<-dba.analyze(H3K4me3_narrow) ### error massage: "Repeated column names found in count matrix"

best

sajjad