Hi,
I am new to DESeq2 and I am trying to apply it to a RNA-seq data derived from TCGA. Everything goes fine until I need to call the results() function and I obtain this error:
Error in `rownames<-`(`*tmp*`, value = c("chr1:12227:+,chr1:12595:+", :
duplicate rownames not allowed
With these being the first 10 row names:
> mat.rnames[1:10]
[1] "chr1:12227:+,chr1:12595:+" "chr1:12227:+,chr1:12613:+" "chr1:12227:+,chr1:12646:+" "chr1:12697:+,chr1:13221:+"
[5] "chr1:12721:+,chr1:13221:+" "chr1:12721:+,chr1:13403:+" "chr1:14829:-,chr1:14970:-" "chr1:14829:-,chr1:15796:-"
[9] "chr1:15038:-,chr1:15796:-" "chr1:15942:-,chr1:16607:-"
Perhaps it's getting confused because the first part of a portion of the strings are the same. I've researched extensively on the subject but haven't yet found a solution or a workaround. Any help or insight would be greatly appreciated.
Here's my sessionInfo() fyi:
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.14.2 DESeq2_1.4.5 RcppArmadillo_0.4.300.8.0 Rcpp_0.11.2
[5] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.9 BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] annotate_1.42.0 AnnotationDbi_1.26.0 Biobase_2.24.0 DBI_0.2-7 genefilter_1.46.1
[6] geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29 locfit_1.5-9.1 RColorBrewer_1.0-5
[11] RSQLite_0.11.4 splines_3.1.0 stats4_3.1.0 survival_2.37-7 tools_3.1.0
[16] XML_3.98-1.1 xtable_1.7-3 XVector_0.4.0
Thank you!
Andrew
I am new to DESeq2 and I am trying to apply it to a RNA-seq data derived from TCGA. Everything goes fine until I need to call the results() function and I obtain this error:
Error in `rownames<-`(`*tmp*`, value = c("chr1:12227:+,chr1:12595:+", :
duplicate rownames not allowed
With these being the first 10 row names:
> mat.rnames[1:10]
[1] "chr1:12227:+,chr1:12595:+" "chr1:12227:+,chr1:12613:+" "chr1:12227:+,chr1:12646:+" "chr1:12697:+,chr1:13221:+"
[5] "chr1:12721:+,chr1:13221:+" "chr1:12721:+,chr1:13403:+" "chr1:14829:-,chr1:14970:-" "chr1:14829:-,chr1:15796:-"
[9] "chr1:15038:-,chr1:15796:-" "chr1:15942:-,chr1:16607:-"
Perhaps it's getting confused because the first part of a portion of the strings are the same. I've researched extensively on the subject but haven't yet found a solution or a workaround. Any help or insight would be greatly appreciated.
Here's my sessionInfo() fyi:
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.14.2 DESeq2_1.4.5 RcppArmadillo_0.4.300.8.0 Rcpp_0.11.2
[5] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.9 BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] annotate_1.42.0 AnnotationDbi_1.26.0 Biobase_2.24.0 DBI_0.2-7 genefilter_1.46.1
[6] geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29 locfit_1.5-9.1 RColorBrewer_1.0-5
[11] RSQLite_0.11.4 splines_3.1.0 stats4_3.1.0 survival_2.37-7 tools_3.1.0
[16] XML_3.98-1.1 xtable_1.7-3 XVector_0.4.0
Thank you!
Andrew
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