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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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groupGO() returned no results on R(3.5.1), meanwhile R(3.4.4) return ideal groups #177

Closed kehuachen closed 5 years ago

kehuachen commented 5 years ago

Hi, GuangchuangYu. Recently, I was using ClusterProfiler to analysis several gene datasets, but none of the commands returned any results, even groupGO(). Is this an internet issues? But the WiFi worked find and I even tried college internet with several data access. All the packages and R is the new version. Strangely, I sent the same dataset to my friend's laptop and run groupGO() on R(3.4.4). There were many groups results and it is the right ones since I looked them up on DAVID. What went wrong?

>library(clusterProfiler)
clusterProfiler v3.10.1  For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Warning messages:
1: package ‘ballgown’ was built under R version 3.5.2 
2: package ‘edgeR’ was built under R version 3.5.2 
>library(enrichplot)
>library(org.Hs.eg.db)
> a1
 [1] "4987"      "440073"    "9501"      "147199"    "653635"    "728262"    "774"       "100287171" "118813"    "3607"     
[11] "124565"    "219931"    "170690"    "23654"     "102723924" "208"       "54102"     "7161"      "2794"      "6532"     
[21] "9933"      "9951"      "339184"    "5062"      "101927156" "23129"     "64077"     "9531"      "23371"     "64866"    
[31] "8578"      "1307"      "255758"    "4536"      "85441"     "375260"    "10451"     "100288175"
> a1_ggo=groupGO(gene = a1,OrgDb = org.Hs.eg.db,ont='MF',readable = T,level = 2)
Loading required package: DOSE
DOSE v3.8.0  For help: https://guangchuangyu.github.io/DOSE
If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609
> head(a1_ggo)
[1] ID          Description Count       GeneRatio   geneID     
<0 行> (或0-长度的row.names)
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
 [1] DOSE_3.8.0             org.Hs.eg.db_3.7.0     AnnotationDbi_1.44.0   IRanges_2.16.0         S4Vectors_0.20.1      
 [6] Biobase_2.42.0         BiocGenerics_0.28.0    enrichplot_1.2.0       clusterProfiler_3.10.1 edgeR_3.24.3          
[11] limma_3.38.3           ballgown_2.14.1       

loaded via a namespace (and not attached):
  [1] ChIPseeker_1.18.0                       backports_1.1.3                        
  [3] Hmisc_4.1-1                             fastmatch_1.1-0                        
  [5] plyr_1.8.4                              igraph_1.2.2                           
  [7] lazyeval_0.2.1                          splines_3.5.0                          
  [9] BiocParallel_1.16.5                     GenomeInfoDb_1.18.1                    
 [11] ggplot2_3.1.0                           gridBase_0.4-7                         
 [13] sva_3.30.1                              urltools_1.7.1                         
 [15] digest_0.6.18                           htmltools_0.3.6                        
 [17] GOSemSim_2.8.0                          viridis_0.5.1                          
 [19] GO.db_3.7.0                             gdata_2.18.0                           
 [21] magrittr_1.5                            checkmate_1.8.5                        
 [23] memoise_1.1.0                           cluster_2.0.7-1                        
 [25] Biostrings_2.50.2                       annotate_1.60.0                        
 [27] matrixStats_0.54.0                      prettyunits_1.0.2                      
 [29] colorspace_1.3-2                        blob_1.1.1                             
 [31] ggrepel_0.8.0                           xfun_0.4                               
 [33] dplyr_0.7.8                             crayon_1.3.4                           
 [35] RCurl_1.95-4.11                         jsonlite_1.6                           
 [37] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 genefilter_1.64.0                      
 [39] bindr_0.1.1                             survival_2.43-3                        
 [41] glue_1.3.0                              gtable_0.2.0                           
 [43] zlibbioc_1.28.0                         XVector_0.22.0                         
 [45] UpSetR_1.3.3                            DelayedArray_0.8.0                     
 [47] scales_1.0.0                            DESeq_1.34.1                           
 [49] DBI_1.0.0                               Rcpp_1.0.0                             
 [51] plotrix_3.7-4                           viridisLite_0.3.0                      
 [53] xtable_1.8-3                            progress_1.2.0                         
 [55] htmlTable_1.13.1                        units_0.6-2                            
 [57] gridGraphics_0.3-0                      foreign_0.8-71                         
 [59] bit_1.1-14                              europepmc_0.3                          
 [61] Formula_1.2-3                           htmlwidgets_1.3                        
 [63] httr_1.4.0                              fgsea_1.8.0                            
 [65] gplots_3.0.1                            RColorBrewer_1.1-2                     
 [67] acepack_1.4.1                           pkgconfig_2.0.2                        
 [69] XML_3.98-1.16                           farver_1.1.0                           
 [71] nnet_7.3-12                             locfit_1.5-9.1                         
 [73] ggplotify_0.0.3                         tidyselect_0.2.5                       
 [75] rlang_0.3.0.1                           reshape2_1.4.3                         
 [77] munsell_0.5.0                           tools_3.5.0                            
 [79] RSQLite_2.1.1                           ggridges_0.5.1                         
 [81] stringr_1.3.1                           knitr_1.21                             
 [83] bit64_0.9-7                             caTools_1.17.1.1                       
 [85] purrr_0.2.5                             ggraph_1.0.2                           
 [87] bindrcpp_0.2.2                          nlme_3.1-137                           
 [89] DO.db_2.9                               xml2_1.2.0                             
 [91] biomaRt_2.38.0                          compiler_3.5.0                         
 [93] rstudioapi_0.8                          tibble_1.4.2                           
 [95] tweenr_1.0.1                            geneplotter_1.60.0                     
 [97] stringi_1.2.4                           GenomicFeatures_1.34.1                 
 [99] lattice_0.20-38                         Matrix_1.2-15                          
[101] pillar_1.3.1                            triebeard_0.3.0                        
[103] data.table_1.11.8                       cowplot_0.9.4                          
[105] bitops_1.0-6                            rtracklayer_1.42.1                     
[107] GenomicRanges_1.34.0                    qvalue_2.14.0                          
[109] R6_2.3.0                                latticeExtra_0.6-28                    
[111] KernSmooth_2.23-15                      gridExtra_2.3                          
[113] boot_1.3-20                             MASS_7.3-51.1                          
[115] gtools_3.8.1                            assertthat_0.2.0                       
[117] SummarizedExperiment_1.12.0             DESeq2_1.22.2                          
[119] GenomicAlignments_1.18.1                Rsamtools_1.34.0                       
[121] GenomeInfoDbData_1.2.0                  mgcv_1.8-26                            
[123] hms_0.4.2                               grid_3.5.0                             
[125] rpart_4.1-13                            tidyr_0.8.2                            
[127] rvcheck_0.1.3                           ggforce_0.1.3                          
[129] scatterplot3d_0.3-41                    base64enc_0.1-3
GuangchuangYu commented 5 years ago

thanks for your report, this is a bug of DOSE and has been fixed.

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