Question: Unable to find an inherited method for function 'results' for signature '"DESeqDataSet"'
0
gravatar for shintzen
10 months ago by
shintzen0
shintzen0 wrote:

I am getting an error about results function not being found. I have run this in days past but I had to restart my computer and now it isn't working. I tried reloading packages with:

> source("https://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
biocLite(pkgs, type="source")

I'm following the instructions found here: https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html and the code looks like this:

> dds <- DESeq(dds)
res <- results(dds)

But I can't figure out why there is an issue now. Thanks for any help

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

> Matrix products: default

> locale:
[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] grid      parallel  stats4    stats     graphics  grDevices utils     datasets 
 [9] methods   base     

> other attached packages:
 [1] BiocInstaller_1.30.0        msigdbr_6.2.1               tibble_2.0.1               
 [4] EGSEAdata_1.8.0             EGSEA_1.10.1                pathview_1.22.1            
 [7] topGO_2.34.0                SparseM_1.77                GO.db_3.7.0                
[10] gage_2.32.1                 GSEABase_1.44.0             graph_1.60.0               
[13] annotate_1.60.0             XML_3.98-1.16               systemPipeR_1.16.1         
[16] fission_1.2.0               RUVSeq_1.16.1               edgeR_3.24.3               
[19] limma_3.38.3                EDASeq_2.16.3               ShortRead_1.40.0           
[22] sva_3.30.1                  mgcv_1.8-26                 nlme_3.1-137               
[25] Gviz_1.26.4                 ReportingTools_2.22.1       knitr_1.21                 
[28] org.Hs.eg.db_3.7.0          genefilter_1.64.0           apeglm_1.4.2               
[31] ggbeeswarm_0.6.0            PoiClaClu_1.0.2.1           RColorBrewer_1.1-2         
[34] pheatmap_1.0.12             dplyr_0.7.8                 hexbin_1.27.2              
[37] vsn_3.50.0                  DESeq2_1.22.2               GenomicAlignments_1.18.1   
[40] Rsamtools_1.34.0            Biostrings_2.50.2           XVector_0.22.0             
[43] ggplot2_3.1.0               GenomicFeatures_1.34.1      AnnotationDbi_1.44.0       
[46] biomaRt_2.38.0              SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
[49] BiocParallel_1.16.5         matrixStats_0.54.0          Biobase_2.42.0             
[52] GenomicRanges_1.34.0        GenomeInfoDb_1.16.0         IRanges_2.16.0             
[55] S4Vectors_0.20.1            BiocGenerics_0.26.0        

> loaded via a namespace (and not attached):
  [1] sendmailR_1.2-1           rtracklayer_1.42.1        AnnotationForge_1.24.0   
  [4] Glimma_1.8.2              KEGG.db_3.2.3             GGally_1.4.0             
  [7] R.methodsS3_1.7.1         coda_0.19-2               tidyr_0.8.2              
 [10] pkgmaker_0.27             acepack_1.4.1             bit64_0.9-7              
 [13] aroma.light_3.10.0        R.utils_2.7.0             PFAM.db_3.7.0            
 [16] data.table_1.12.0         rpart_4.1-13              hwriter_1.3.2            
 [19] KEGGREST_1.20.2           RCurl_1.95-4.11           AnnotationFilter_1.4.0   
 [22] org.Mm.eg.db_3.7.0        metap_1.0                 preprocessCore_1.44.0    
 [25] RSQLite_2.1.1             bit_1.1-14                httpuv_1.4.5.1           
 [28] assertthat_0.2.0          xfun_0.4                  hms_0.4.2                
 [31] promises_1.0.1            progress_1.2.0            caTools_1.17.1.1         
 [34] Rgraphviz_2.26.0          DBI_1.0.0                 geneplotter_1.60.0       
 [37] htmlwidgets_1.3           reshape_0.8.8             purrr_0.2.5              
 [40] backports_1.1.3           BatchJobs_1.7             gbRd_0.4-11              
 [43] PADOG_1.24.0              HTMLUtils_0.1.7           ensembldb_2.6.3          
 [46] withr_2.1.2               globaltest_5.36.0         BSgenome_1.50.0          
 [49] checkmate_1.9.1           prettyunits_1.0.2         cluster_2.0.7-1          
 [52] lazyeval_0.2.1            crayon_1.3.4              labeling_0.3             
 [55] pkgconfig_2.0.2           vipor_0.4.5               ProtGenerics_1.12.0      
 [58] nnet_7.3-12               GSA_1.03                  bindr_0.1.1              
 [61] rlang_0.3.1               registry_0.5              affyio_1.52.0            
 [64] GOstats_2.48.0            dichromat_2.0-0           GSVA_1.30.0              
 [67] rngtools_1.3.1            Matrix_1.2-15             base64enc_0.1-3          
 [70] beeswarm_0.2.3            viridisLite_0.3.0         png_0.1-7                
 [73] rjson_0.2.20              bitops_1.0-6              R.oo_1.22.0              
 [76] KernSmooth_2.23-15        blob_1.1.1                R2HTML_2.3.2             
 [79] doRNG_1.7.1               stringr_1.3.1             brew_1.0-6               
 [82] scales_1.0.0              memoise_1.1.0             magrittr_1.5             
 [85] plyr_1.8.4                safe_3.22.0               gplots_3.0.1             
 [88] bibtex_0.4.2              gdata_2.18.0              zlibbioc_1.28.0          
 [91] compiler_3.5.0            bbmle_1.0.20              KEGGgraph_1.40.0         
 [94] affy_1.60.0               Category_2.48.0           htmlTable_1.13.1         
 [97] Formula_1.2-3             MASS_7.3-51.1             tidyselect_0.2.5         
[100] stringi_1.2.4             emdbook_1.3.10            yaml_2.2.0               
[103] locfit_1.5-9.1            latticeExtra_0.6-28       VariantAnnotation_1.28.10
[106] tools_3.5.0               rstudioapi_0.9.0          foreach_1.4.4            
[109] foreign_0.8-71            gridExtra_2.3             digest_0.6.18            
[112] BiocManager_1.30.4        shiny_1.2.0               bindrcpp_0.2.2           
[115] Rcpp_1.0.0                later_0.7.5               OrganismDbi_1.24.0       
[118] httr_1.4.0                ggbio_1.30.0              biovizBase_1.30.1        
[121] Rdpack_0.10-1             colorspace_1.4-0          splines_3.5.0            
[124] RBGL_1.58.1               shinythemes_1.1.2         plotly_4.8.0             
[127] xtable_1.8-3              jsonlite_1.6              BBmisc_1.11              
[130] R6_2.3.0                  Hmisc_4.1-1               KEGGdzPathwaysGEO_1.18.0 
[133] pillar_1.3.1              htmltools_0.3.6           mime_0.6                 
[136] hgu133plus2.db_3.2.3      glue_1.3.0                DT_0.5                   
[139] DESeq_1.34.1              codetools_0.2-16          lattice_0.20-38          
[142] numDeriv_2016.8-1         hgu133a.db_3.2.3          curl_3.3                 
[145] gtools_3.8.1              survival_2.43-3           org.Rn.eg.db_3.7.0       
[148] munsell_0.5.0             GenomeInfoDbData_1.1.0    iterators_1.0.10         
[151] reshape2_1.4.3            gtable_0.2.0
deseq2 • 246 views
ADD COMMENTlink modified 10 months ago by Michael Love26k • written 10 months ago by shintzen0
Answer: Unable to find an inherited method for function 'results' for signature '"DESeqD
2
gravatar for Michael Love
10 months ago by
Michael Love26k
United States
Michael Love26k wrote:

Have you loaded DESeq2?

ADD COMMENTlink written 10 months ago by Michael Love26k

I have with library(DESeq2) and there is no issue on load

ADD REPLYlink written 10 months ago by shintzen0
1

Another thing is if another package masked results(), which it would have mentioned on load. Then you should use DESeq2::results()

ADD REPLYlink written 10 months ago by Michael Love26k

This worked, I didn't notice a package masking it on load. Do you have any resources to share about packages that get masked? I would like to know how to prevent this

ADD REPLYlink written 10 months ago by shintzen0

If you load two packages that both export a function of the same name, then one masks the other and R prints a message on load of the second package. There is a package called "conflicted" which attempts to alleviate this a bit.

ADD REPLYlink written 10 months ago by Michael Love26k
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