Repeated column names found in count matrix
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Entering edit mode
@khanisajjad-9137
Last seen 6.0 years ago
Germany

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

 

 

diffbind • 1.8k views
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Entering edit mode

Hi,

One possibility is that you have duplicated sample IDs in your sample sheet.  If you do, try making them unique.  Or you can send the sample sheet to me so I can have a look at it and try to reproduce the error.  My email address can be found on the DiffBind page:

http://bioconductor.org/packages/release/bioc/html/DiffBind.html

Cheers,

 - Gord

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