Differences between clusterProfiler and agriGO

Hi Guangchuang,

When I'm using clusterprofiler, I got different results compared to agriGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php) using the same set of genes.

For example GO:0006412, in the clusterprofiler result 94 out of 2691 belong to this term. In agriGO results, 170 out of 2614 belong to this term. I'm wondering whether you have any idea why this happens? Thanks. See the results below: test_agriGO_results.txt test_clusterprofier.BP.txt

I attached the files and code, as well as the session information here.

Files used clusterprofiler. gene.list.txt test.BP.GENE.txt test.BP.NAME.txt

Files for agriGO: test4agrigo.txt forTest.gitb.BP.txt

library(clusterProfiler)
PREFIX="test"
term2GENE <- paste(PREFIX, i, "GENE.txt", sep = ".")
term2NAME <- paste(PREFIX, i, "NAME.txt", sep = ".")
cat(term2GENE, "\n")
cat(term2NAME, "\n")
term2gene <- read.table(term2GENE, sep = "\t")
term2name <- read.delim(term2NAME, sep = "\t")
gene_list = read.table("gene.list.txt")
geneid_sig = as.vector(gene_list$V1)
res <- enricher(geneid_sig, TERM2GENE=term2gene, TERM2NAME=term2name,
                pvalueCutoff = 1, qvalueCutoff = 1)
res_df <- as.data.frame(res)
write.table(res_df, "test_clusterprofier.BP.txt", sep="\t", quote=F, col.names = T, row.names=F)
sessionInfo()

 sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.30.0   gridExtra_2.3          ggplot2_3.1.0          clusterProfiler_3.10.0

loaded via a namespace (and not attached):
 [1] Biobase_2.42.0       viridis_0.5.1        httr_1.3.1           tidyr_0.8.2          bit64_0.9-7         
 [6] jsonlite_1.5         viridisLite_0.3.0    splines_3.5.1        ggraph_1.0.2         assertthat_0.2.0    
[11] DO.db_2.9            rvcheck_0.1.1        triebeard_0.3.0      urltools_1.7.1       stats4_3.5.1        
[16] blob_1.1.1           progress_1.2.0       ggrepel_0.8.0        pillar_1.3.0         RSQLite_2.1.1       
[21] lattice_0.20-35      glue_1.3.0           digest_0.6.18        RColorBrewer_1.1-2   qvalue_2.14.0       
[26] colorspace_1.3-2     cowplot_0.9.3        Matrix_1.2-14        plyr_1.8.4           pkgconfig_2.0.2     
[31] purrr_0.2.5          GO.db_3.7.0          scales_1.0.0         ggplotify_0.0.3      europepmc_0.3       
[36] tweenr_1.0.0         enrichplot_1.2.0     BiocParallel_1.16.0  ggforce_0.1.3        tibble_1.4.2        
[41] farver_1.0           IRanges_2.16.0       withr_2.1.2          UpSetR_1.3.3         BiocGenerics_0.28.0 
[46] lazyeval_0.2.1       magrittr_1.5         crayon_1.3.4         memoise_1.1.0        DOSE_3.8.0          
[51] MASS_7.3-50          xml2_1.2.0           prettyunits_1.0.2    tools_3.5.1          data.table_1.11.8   
[56] hms_0.4.2            stringr_1.3.1        S4Vectors_0.20.0     munsell_0.5.0        AnnotationDbi_1.44.0
[61] bindrcpp_0.2.2       compiler_3.5.1       gridGraphics_0.3-0   rlang_0.3.0.1        ggridges_0.5.1      
[66] units_0.6-1          igraph_1.2.2         labeling_0.3         gtable_0.2.0         DBI_1.0.0           
[71] reshape2_1.4.3       R6_2.3.0             dplyr_0.7.7          bit_1.1-14           bindr_0.1.1         
[76] fastmatch_1.1-0      fgsea_1.8.0          GOSemSim_2.8.0       stringi_1.2.4        parallel_3.5.1      
[81] Rcpp_0.12.19         tidyselect_0.2.5

YuLab-SMU / clusterProfiler

Differences between clusterProfiler and agriGO #171