DESeq2 Results Error: Duplicate Rownames Not Allowed

[araschenbrenner]

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

[Michael Love]

hi Andrew,

At the results() step, the software needs to build a DataFrame, and will put the rownames(dds) as rownames to identify each gene. It looks like the SummarizedExperiment allows duplicate rownames but not DataFrame.

Is there a way you can name the genes such that they are unique? This seems desirable in general for your analysis.

Check:

rownames(dds)

These are usually coming from the rownames of the count matrix. How did you build the count matrix?

[Michael Love]

fyi I've fixed this in the development version. For rownames "gene, gene, gene" it will message user and turn duplicate rownames into "gene, gene.1, gene.2".

[araschenbrenner]

Sorry for the late reply, my attention was pulled away from this.

The count matrix was built from combining single patient files from TCGA RNA-seq raw count data. For each patient, the data file gives the chromosome start and end location (e.g. chr1:12227:+,chr1:12595:+) and an integer count.

I was under the impression that the row names here were unique, but what I thought might not be unique is the first part of the some of the row names. For example,

"chr1:12227:+,chr1:12595:+"
"chr1:12227:+,chr1:12613:+"
"chr1:12227:+,chr1:12646:+"

Up until the comma here, the strings are the same.

I may be able to start an unique index, which would likely fix the problem of duplicate row names.

Have you released this version with this revision on bioconductor? Thanks for your help!

Andrew

[Michael Love]

You can check what might be duplicated with:

rn = rownames(dds)
rn[duplicated(rn)]

In Bioconductor, other than "show stopping bugs", all changes to packages goes into the development branch, which is released and becomes the release branch every 6 months (April/October). The idea is so that users can work with a stable set of packages which have higher interdependence.