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Question: clusterProfiler compareCluster enrichDAVID
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gravatar for Gilgi
27 days ago by
Gilgi10
European Union
Gilgi10 wrote:

Hello,

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

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] 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            org.Hs.eg.db_3.5.0      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:

data(gcSample)
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
1
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.

http://guangchuangyu.github.io/2016/11/showcategory-parameter-for-visualizing-comparecluster-output/

 

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
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