ClusterProfiler: enrichGO / compareCluster and Pvalue threeshold
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@samuel-collombet-6574
Last seen 4.4 years ago
France

Hi,

I am using ClusterProfiler to compare GO therm enrichment between genes clusters. With enrichGO() or compareCluster(), if I put a pvalue threeshold of 1,  nothing is reported for a specific GO term and a specific cluster (no corresponding line in the summary of the result), this mean that there were no overlap at all between the cluster and the GO-term gene set? 

clusterprofiler • 2.2k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

Hi,

> CompareGO <- compareCluster(ClusterList, pvalueCutoff=1,readable=T, organism="mouse", pAdjustMethod="none", fun="enrichGO",ont="BP" )
> Sum<-summary(CompareGO)


> Sum[Sum$ID=="GO:0010498",1:4]
     Cluster         ID                           Description GeneRatio
544        1 GO:0010498 proteasomal protein catabolic process     7/372
5223       7 GO:0010498 proteasomal protein catabolic process     9/376
7136       9 GO:0010498 proteasomal protein catabolic process     7/668

 

In this example, there is no genes annotated by GO:0010498 in clusters 2:6 and 8.

 

Please also bare in mind, enrichGO contains a parameter minGSSize with default value of 5, so there maybe some clusters have genes annotated by GO:0010498 but the gene number is lower than 5 and was omitted. Of course, you can set minGSSize = 1.

 

Bests,

Guangchuang

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Thanks that is what I thought :)

Thanks for the precision about minGSSize, I thought this was the min Size of the Gene set in the annotation (ie no GO therm are consider if they contain less than minGSSize genes). 

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

Can you post an example?

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@samuel-collombet-6574
Last seen 4.4 years ago
France

Hi Guangchuang Yu, 

Here is an example:

> CompareGO <- compareCluster(ClusterList, pvalueCutoff=1,readable=T, organism="mouse", pAdjustMethod="none", fun="enrichGO",ont="BP" )
> Sum<-summary(CompareGO)


> Sum[Sum$ID=="GO:0010498",1:4]
     Cluster         ID                           Description GeneRatio
544        1 GO:0010498 proteasomal protein catabolic process     7/372
5223       7 GO:0010498 proteasomal protein catabolic process     9/376
7136       9 GO:0010498 proteasomal protein catabolic process     7/668


> Sum[Sum$ID=="GO:0009790",1:4]
     Cluster         ID        Description GeneRatio
860        2 GO:0009790 embryo development    66/600
2159       3 GO:0009790 embryo development    58/704
3185       5 GO:0009790 embryo development    62/556
4738       6 GO:0009790 embryo development    40/714
5580       7 GO:0009790 embryo development    18/376
5734       8 GO:0009790 embryo development    36/550
7121       9 GO:0009790 embryo development    31/668

I have 9 cluster in total, do you want to ClusterList object?

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] topGO_2.18.0              SparseM_1.6               graph_1.44.1              BiocInstaller_1.16.1      clusterProfiler_2.0.1     reactome.db_1.48.0        ReactomePA_1.10.1        
 [8] GO.db_3.0.0               org.Mm.eg.db_3.0.0        RSQLite_1.0.0             DBI_0.3.1                 AnnotationDbi_1.28.1      Mfuzz_2.26.0              DynDoc_1.44.0            
[15] widgetTools_1.44.0        e1071_1.6-4               Biobase_2.26.0            reshape2_1.4.1            Rsubread_1.16.1           biomaRt_2.22.0            wq_0.4-1                 
[22] zoo_1.7-11                reshape_0.8.5             ggplot2_1.0.0             RColorBrewer_1.1-2        DESeq2_1.6.3              RcppArmadillo_0.4.650.1.1 Rcpp_0.11.4              
[29] GenomicRanges_1.18.4      GenomeInfoDb_1.2.4        IRanges_2.0.1             S4Vectors_0.4.0           BiocGenerics_0.12.1      

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3     annotate_1.44.0     base64enc_0.1-2     BatchJobs_1.5       BBmisc_1.9          BiocParallel_1.0.3  bitops_1.0-6        brew_1.0-6          checkmate_1.5.1    
[10] class_7.3-12        cluster_2.0.1       codetools_0.2-10    colorspace_1.2-4    digest_0.6.8        DO.db_2.8.0         DOSE_2.4.0          fail_1.2            foreach_1.4.2      
[19] foreign_0.8-63      Formula_1.2-0       genefilter_1.48.1   geneplotter_1.44.0  GOSemSim_1.24.1     graphite_1.12.0     gtable_0.1.2        Hmisc_3.15-0        igraph_0.7.1       
[28] iterators_1.0.7     KEGG.db_3.0.0       labeling_0.3        lattice_0.20-30     latticeExtra_0.6-26 locfit_1.5-9.1      MASS_7.3-39         munsell_0.4.2       nnet_7.3-9         
[37] org.Hs.eg.db_3.0.0  plyr_1.8.1          proto_0.3-10        qvalue_1.40.0       RCurl_1.95-4.5      rpart_4.1-9         scales_0.2.4        sendmailR_1.2-1     splines_3.1.2      
[46] stringr_0.6.2       survival_2.38-1     tkWidgets_1.44.0    tools_3.1.2         XML_3.98-1.1        xtable_1.7-4        XVector_0.6.0      

 

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