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Question: Repeated column names found in count matrix
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gravatar for khani.sajjad
2.0 years ago by
Germany
khani.sajjad0 wrote:

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

 

 

ADD COMMENTlink written 2.0 years ago by khani.sajjad0

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

ADD REPLYlink written 2.0 years ago by Gord Brown560
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