[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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