[BioC] edgeR import error

ES [guest] guest at bioconductor.org
Tue Feb 19 10:20:18 CET 2013


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

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