Question: clusterProfiler compareCluster enrichDAVID
gravatar for Gilgi
27 days ago by
European Union
Gilgi10 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 26 days ago by Guido Hooiveld2.2k • written 27 days ago by Gilgi10

any reproducible example of using enrichDAVID that causes Rstudio crash?

ADD REPLYlink written 24 days ago by Guangchuang Yu800

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 23 days ago by Gilgi10
gravatar for Guido Hooiveld
26 days ago by
Guido Hooiveld2.2k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.2k 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 26 days ago by Guido Hooiveld2.2k

Thanks a lot!

ADD REPLYlink written 23 days ago by Gilgi10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 300 users visited in the last hour