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shintzen
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@shintzen-18932
Last seen 5.9 years ago
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
I have with library(DESeq2) and there is no issue on load
Another thing is if another package masked results(), which it would have mentioned on load. Then you should use DESeq2::results()
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
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.