Question: Unable to find an inherited method for function 'results' for signature '"DESeqDataSet"'
gravatar for shintzen
10 months ago by
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("")
pkgs <- rownames(installed.packages())
biocLite(pkgs, type="source")

I'm following the instructions found here: 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]          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]        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        
[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
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

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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