Issue "one-to-many" with org.Hs.eg.db
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Entering edit mode
Nathalie • 0
@6a5d5618
Last seen 5 days ago
France

Hello,

I'm using org.Hs.eg.db (3.12.0) to map my list of genes (ENSEMBL) to get their SYMBOL. However, when I execute the following command, I get this message : 'select()' returned 1:many mapping between keys and columns meaning that some ENSEMBL id are duplicated, such as ENSG00000004866.

ENSG00000004866 ST7

ENSG00000004866 ST7-OT3

On the ENSEMBL website, it's mentionned that ST7-OT3 (NCBI gene (formerly Entrezgene) record; description: ST7 overlapping transcript 3,) is an external reference matched to Gene ENSG00000004866.

Why it's appearing in my list ? How can I manage this issue to get a 1:1 relation ?

Thanks in advance !

ann <- select(org.Hs.eg.db,keys=rownames(dge$counts),keytype="ENSEMBL",columns=c("SYMBOL")) 
#  'select()' returned 1:many mapping between keys and columns



sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] taRifx_1.0.6.2                          arsenal_3.6.2                           reshape2_1.4.4                         
 [4] Glimma_2.0.0                            knitr_1.33                              biomaRt_2.46.3                         
 [7] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.12.0                    
[10] GO.db_3.12.1                            OrganismDbi_1.32.0                      GenomicFeatures_1.42.3                 
[13] AnnotationDbi_1.52.0                    mixOmics_6.12.2                         lattice_0.20-41                        
[16] MASS_7.3-53                             RColorBrewer_1.1-2                      magrittr_2.0.1                         
[19] openxlsx_4.2.3                          forcats_0.5.1                           stringr_1.4.0                          
[22] dplyr_1.0.5                             purrr_0.3.4                             readr_1.4.0                            
[25] tidyr_1.1.3                             tibble_3.1.1                            ggplot2_3.3.3                          
[28] tidyverse_1.3.1                         DESeq2_1.30.1                           SummarizedExperiment_1.18.2            
[31] DelayedArray_0.16.3                     MatrixGenerics_1.2.1                    matrixStats_0.58.0                     
[34] Matrix_1.2-18                           Biobase_2.50.0                          GenomicRanges_1.40.0                   
[37] GenomeInfoDb_1.26.7                     IRanges_2.24.1                          S4Vectors_0.28.1                       
[40] BiocGenerics_0.36.1                     edgeR_3.32.1                            limma_3.46.0
org.Hs.eg.db • 104 views
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Entering edit mode

Probably you'll find the help page of select very useful. There's the argument multiVals to decide what to do in those cases.

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Guido Hooiveld ★ 2.9k
@guido-hooiveld-2020
Last seen 13 hours ago
Wageningen University, Wageningen, the …

.... and since your primary IDs are ENSEMBL ids; why don't you use an EnsDB (instead of a NCBI-based OrgDb) for annotating? This thread may be useful to get started with an EnsDb.

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Many thanks for pointing to EnsDB. I never knew about having a specific Ensembl data package!

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