Question: clusterProfiler compareCluster enrichDAVID
gravatar for GFM
12 months ago by
European Union
GFM20 wrote:


I have some questions regarding the use of the clusterProfiler package:

1. In the compare dotplot - which categories are chosen to be shown - are these the top functions that had the lowest p-value in any of the clusters?

2. In the compare dotplot – what is the number in parentheses in the x-axis for each cluster?

3. Is it possible to run enrichDAVID when running Rstudio on a PC? It causes the R session to crash.

Thanks for the great package.



> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RDAVIDWebService_1.16.0 ggplot2_2.2.1           GOstats_2.44.0          Category_2.44.0        
 [5] Matrix_1.2-11           graph_1.56.0        AnnotationDbi_1.40.0   
 [9] IRanges_2.12.0          S4Vectors_0.16.0        Biobase_2.38.0          BiocGenerics_0.24.0    
[13] clusterProfiler_3.6.0   DOSE_3.4.0             

loaded via a namespace (and not attached):
 [1] qvalue_2.10.0          genefilter_1.60.0      fgsea_1.4.0            reshape2_1.4.2        
 [5] purrr_0.2.4            rJava_0.9-9            splines_3.4.2          lattice_0.20-35       
 [9] colorspace_1.3-2       survival_2.41-3        blob_1.1.0             XML_3.98-1.9          
[13] RBGL_1.54.0            rlang_0.1.4            glue_1.2.0             DBI_0.7               
[17] Rgraphviz_2.22.0       BiocParallel_1.12.0    bit64_0.9-7            rvcheck_0.0.9         
[21] plyr_1.8.4             stringr_1.2.0          munsell_0.4.3          GOSemSim_2.4.0        
[25] gtable_0.2.0           memoise_1.1.0          GSEABase_1.40.0        Rcpp_0.12.13          
[29] xtable_1.8-2           scales_0.5.0           DO.db_2.9              annotate_1.56.1       
[33] bit_1.1-12             gridExtra_2.3          fastmatch_1.1-0        digest_0.6.12         
[37] stringi_1.1.5          grid_3.4.2             tools_3.4.2            bitops_1.0-6          
[41] magrittr_1.5           lazyeval_0.2.1         RCurl_1.95-4.8         tibble_1.3.4          
[45] RSQLite_2.0            GO.db_3.5.0            tidyr_0.7.2            pkgconfig_2.0.1       
[49] data.table_1.10.4-3    AnnotationForge_1.20.0 igraph_1.1.2           compiler_3.4.2        



ADD COMMENTlink modified 12 months ago by Guido Hooiveld2.3k • written 12 months ago by GFM20

any reproducible example of using enrichDAVID that causes Rstudio crash?

ADD REPLYlink written 12 months ago by Guangchuang Yu1.1k

Thanks a lot.

Here is the code:

david <- enrichDAVID(gene = gcSample[["X1"]],
                     idType = "ENTREZ_GENE_ID",
                     annotation = "GOTERM_BP_FAT",
                     david.user = "my_mail")

(I have registered in DAVID)


The session crashes with the following error message:

Failed to write core dump. Minidumps are not enabled by default on client versions of Windows

ADD REPLYlink written 11 months ago by GFM20
gravatar for Guido Hooiveld
12 months ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k wrote:

1): These are indeed based on significance. See also this post of Guangchuang.


2): AFAIK the number of genes in each cluster.


3): I am sorry, but I don't know. (I don't use R studio).


ADD COMMENTlink written 12 months ago by Guido Hooiveld2.3k

Thanks a lot!

ADD REPLYlink written 11 months ago by GFM20
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