change a column within a DESeq results object
Entering edit mode
Matt • 0
Last seen 8 weeks ago
United States

Error : Error in .testForValidKeys(x, keys, keytype, fks) :

None of the keys entered are valid keys for 'MGI'. Please use the keys method to see a listing of valid arguments.

#Gene ID using AnnotationDBi

counts_Ji = read.table("Raw_count_ControlvsLPS.txt",header=T)

counts_Ji = #already df

counts_Ji = mapIds(, keys=rownames(counts_Ji), keytype = "MGI", column=c("SYMBOL"))


sessionInfo( )

```R version 4.1.3 (2022-03-10)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 19042)

Matrix products: default


[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         

[5] LC_TIME=English_United States.1252   

attached base packages:

[1] stats4    stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:

[1] ReportingTools_2.34.0       knitr_1.39                  EnhancedVolcano_1.12.0      ggrepel_0.9.1             

 [5] gplots_3.1.3                ggplot2_3.3.6               dplyr_1.0.9                 pheatmap_1.0.12           

 [9] DESeq2_1.34.0               SummarizedExperiment_1.24.0 MatrixGenerics_1.6.0        matrixStats_0.62.0        

[13]         AnnotationForge_1.36.0      ensembldb_2.18.4            AnnotationFilter_1.18.0   

[17] GenomicFeatures_1.46.5      AnnotationDbi_1.56.2        Biobase_2.54.0              GenomicRanges_1.46.1      

[21] GenomeInfoDb_1.30.1         IRanges_2.28.0              S4Vectors_0.32.4            AnnotationHub_3.2.2       

[25] BiocFileCache_2.2.1         dbplyr_2.2.0                BiocGenerics_0.40.0       

loaded via a namespace (and not attached):

  [1] utf8_1.2.2                    R.utils_2.11.0                tidyselect_1.1.2            

  [4] RSQLite_2.2.14                htmlwidgets_1.5.4             grid_4.1.3                  

  [7] BiocParallel_1.28.3           munsell_0.5.0                 withr_2.5.0                 

 [10] colorspace_2.0-3              Category_2.60.0               filelock_1.0.2              

 [13] OrganismDbi_1.36.0            ggalt_0.4.0                   rstudioapi_0.13             

 [16] Rttf2pt1_1.3.10               labeling_0.4.2                GenomeInfoDbData_1.2.7      

 [19] hwriter_1.3.2.1               bit64_4.0.5                   farver_2.1.0                

 [22] vctrs_0.4.1                   generics_0.1.2                xfun_0.31                   

 [25] biovizBase_1.42.0             R6_2.5.1                      ggbeeswarm_0.6.0            

 [28] locfit_1.5-9.5                bitops_1.0-7                  cachem_1.0.6                

 [31] reshape_0.8.9                 DelayedArray_0.20.0           assertthat_0.2.1            

 [34] promises_1.2.0.1              BiocIO_1.4.0                  scales_1.2.0                

 [37] nnet_7.3-17                   beeswarm_0.4.0                gtable_0.3.0                

 [40] ash_1.0-15                    ggbio_1.42.0                  rlang_1.0.2                 

 [43] genefilter_1.76.0             splines_4.1.3                 rtracklayer_1.54.0          

 [46] extrafontdb_1.0               lazyeval_0.2.2                dichromat_2.0-0.1           

 [49] checkmate_2.1.0               BiocManager_1.30.18           yaml_2.3.5                  

 [52] reshape2_1.4.4                backports_1.4.1               httpuv_1.6.5                

 [55] Hmisc_4.7-0                   RBGL_1.70.0                   extrafont_0.18              

 [58] tools_4.1.3                   ellipsis_0.3.2                RColorBrewer_1.1-3          

 [61] Rcpp_1.0.8.3                  plyr_1.8.7                    base64enc_0.1-3             

 [64] progress_1.2.2                zlibbioc_1.40.0               purrr_0.3.4                 

 [67] RCurl_1.98-1.6                prettyunits_1.1.1             rpart_4.1.16                

 [70] cluster_2.1.2                 magrittr_2.0.3                data.table_1.14.2           

 [73] ProtGenerics_1.26.0           hms_1.1.1                     mime_0.12                   

 [76] xtable_1.8-4                  XML_3.99-0.9                  jpeg_0.1-9                  

 [79] gridExtra_2.3                 compiler_4.1.3                biomaRt_2.50.3              

 [82] tibble_3.1.7                  maps_3.4.0                    KernSmooth_2.23-20          

 [85] crayon_1.5.1                  R.oo_1.24.0                   htmltools_0.5.2             

 [88] GOstats_2.60.0                later_1.3.0                   Formula_1.2-4               

 [91] geneplotter_1.72.0            DBI_1.1.2                     proj4_1.0-11                

 [94] MASS_7.3-55                   rappdirs_0.3.3                Matrix_1.4-0                

 [97] cli_3.3.0                     R.methodsS3_1.8.1             parallel_4.1.3              

[100] pkgconfig_2.0.3               GenomicAlignments_1.30.0      foreign_0.8-82              

[103] xml2_1.3.3                    annotate_1.72.0               vipor_0.4.5                 

[106] XVector_0.34.0                stringr_1.4.0                 VariantAnnotation_1.40.0    

[109] digest_0.6.29                 graph_1.72.0                  Biostrings_2.62.0           

[112] htmlTable_2.4.0               edgeR_3.36.0                  GSEABase_1.56.0             

[115] restfulr_0.0.13               curl_4.3.2                    shiny_1.7.1                 

[118] Rsamtools_2.10.0              gtools_3.9.2.1                rjson_0.2.21                

[121] lifecycle_1.0.1               PFAM.db_3.14.0                limma_3.50.3                

[124] BSgenome_1.62.0               fansi_1.0.3                   pillar_1.7.0                

[127] lattice_0.20-45               GGally_2.1.2                  ggrastr_1.0.1               

[130] KEGGREST_1.34.0               fastmap_1.1.0                 httr_1.4.3                  

[133] survival_3.2-13               GO.db_3.14.0                  interactiveDisplayBase_1.32.0

[136] glue_1.6.2                    png_0.1-7                     BiocVersion_3.14.0          

[139] bit_4.0.4                     Rgraphviz_2.38.0              stringi_1.7.6               

[142] blob_1.2.3                    latticeExtra_0.6-29           caTools_1.18.2              

[145] memoise_2.0.1
EnhancedVolcano • 167 views
Entering edit mode

Could you elaborate a bit more the problem ? The title of the post does not fit with the code provided

Entering edit mode

Yes I am sorry I must have accidentally forgot to change the title. I am trying to get the gene symbols based on ENSEMBL ID using AnnotationDbi. However it says the keytype I am using is not valid. Which is not true. I have used the listkey function and copied the output I want (ENSEMBL) yet I get there error which is above. You will notice I also tried to use keytype "MGI" which is also invalid.

Entering edit mode

Few remarks:

** keytypes will allow you to check what you can query with. ENSEMBL (3rd keytype) is to be used when having ENSEMBL IDs, and SYMBOL the column to retrieve gene symbols.

** Note that contains annotation info that is NCBI-based. So if you have used ENSEMBL/GENCODE-based FASTA and GTF files used for mapping your sequence reads, I would recommend to rather use ENSEMBL-based (EnsDb) annotations (by doing so you thus 'stay' in the same eco-system).

> ensids <- c("ENSMUSG00000000001", "ENSMUSG00000000003", "ENSMUSG00000000028",
+             "ENSMUSG00000000031", "ENSMUSG00000000037", "ENSMUSG00000000049")
> # using (= based on NCBI gene IDs)
> library(
> keytypes(
 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT" 
 [9] "EVIDENCEALL"  "GENENAME"     "GENETYPE"     "GO"          
[13] "GOALL"        "IPI"          "MGI"          "ONTOLOGY"    
[17] "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"        
[21] "PROSITE"      "REFSEQ"       "SYMBOL"       "UNIPROT"     
> mapIds(, keys=ensids, keytype = "ENSEMBL", column=c("SYMBOL"))
'select()' returned 1:1 mapping between keys and columns
ENSMUSG00000000001 ENSMUSG00000000003 ENSMUSG00000000028 ENSMUSG00000000031 
           "Gnai3"             "Pbsn"            "Cdc45"              "H19" 
ENSMUSG00000000037 ENSMUSG00000000049 
           "Scml2"             "Apoh" 
> # using EnsDb.Mmusculus.v106 (= based on ENSEMBL IDs)
> library(EnsDb.Mmusculus.v106)
> AnnotationDbi:::select(EnsDb.Mmusculus.v106, keys = ensids, keytype = "GENEID",
+     columns = c("SYMBOL") )
              GENEID SYMBOL
1 ENSMUSG00000000001  Gnai3
2 ENSMUSG00000000003   Pbsn
3 ENSMUSG00000000028  Cdc45
4 ENSMUSG00000000031    H19
5 ENSMUSG00000000037  Scml2
6 ENSMUSG00000000049   Apoh

If you would like to use the EnsDb, have a look at this post, and the ones linked to in that post. ENSEMBL to gene symbol


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