edgeR import error
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Guest User ★ 12k
@guest-user-4897
Last seen 7.8 years ago
Hi, I have been trying to create a DGEList object in edgeR, using the following command: > tar<-read.delim("test_target.txt") > b<-readDGE(tar) Error in readDGE(tar) : Repeated tag sequences in tmp1.txt where test target is files groups 1 tmp1.txt fem 2 tmp2.txt fem 3 tmp3.txt male 4 tmp4.txt male and tmp1.txt is a tab delimit text file with 2 columns (col1: geneID, col2: raw counts). target_id uniq_counts 0 51 1 0 10 24 100 13 1000 5 10000 227 10001 7 10002 28 10003 21 I have checked that the geneID/tags are unique using awk '{print$1}' | sort|uniq and yet I keep getting this error. I have used edgeR successfully in the past and am currently also able to use it with other older data files. Thanks E -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 edgeR_3.0.8 limma_3.14.4 loaded via a namespace (and not attached): [1] tools_2.15.2 -- Sent via the guest posting facility at bioconductor.org.
edgeR edgeR • 2.5k views
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@james-w-macdonald-5106
Last seen 18 hours ago
United States
On 2/19/2013 4:20 AM, ES [guest] wrote: > Hi, > > I have been trying to create a DGEList object in edgeR, using the following command: > >> tar<-read.delim("test_target.txt") >> b<-readDGE(tar) > Error in readDGE(tar) : Repeated tag sequences in tmp1.txt > > where test target is > files groups > 1 tmp1.txt fem > 2 tmp2.txt fem > 3 tmp3.txt male > 4 tmp4.txt male > > and tmp1.txt is a tab delimit text file with 2 columns (col1: geneID, col2: raw counts). > > target_id uniq_counts > 0 51 > 1 0 > 10 24 > 100 13 > 1000 5 > 10000 227 > 10001 7 > 10002 28 > 10003 21 > > I have checked that the geneID/tags are unique using awk '{print$1}' | sort|uniq and yet I keep getting this error. Try x <- read.delim("tmp1.txt", stringsAsFactors = FALSE) any(duplicated(x[,1])) and possibly x[duplicated(x[,1]),] because R thinks you have duplicates. Best, Jim > > I have used edgeR successfully in the past and am currently also able to use it with other older data files. > > Thanks > E > > > -- output of sessionInfo(): > > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.3 edgeR_3.0.8 limma_3.14.4 > > loaded via a namespace (and not attached): > [1] tools_2.15.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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