Question: EGSEA generateReport() error "no adj nodes"
0
gravatar for Jenny Drnevich
22 months ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:

Hello,

I am running through the EGSEA123 workflow, except I am using my own human data, consisting of 14K Entrez IDs, all of which are in org.Hs.eg.db. Everything goes fine until I try to generate the report when I get an error during the Build GO DAG topology and some additional warnings:

library(edgeR)
library(org.Hs.eg.db)
library(EGSEAdata)
library(EGSEA)

> dim(v)

[1] 14213    39

> head(v$genes)

     gene_id ENTREZID SYMBOL                                           GENENAME

3043     HBB     3043    HBB                            hemoglobin subunit beta

567      B2M      567    B2M                               beta-2-microglobulin

7178    TPT1     7178   TPT1        tumor protein, translationally-controlled 1

1915  EEF1A1     1915 EEF1A1 eukaryotic translation elongation factor 1 alpha 1

60      ACTB       60   ACTB                                         actin beta

7114  TMSB4X     7114 TMSB4X                          thymosin beta 4, X-linked

> sum(v$genes$ENTREZID %in% keys(org.Hs.eg.db,keytype = "ENTREZID"))

[1] 14213

Loading required package: GenomicRanges

Loading required package: GenomeInfoDb

> generateReport(gsa, number = 20, report.dir="EGSEA_results/report")

EGSEA HTML report is being generated ...

##------ Thu Nov 30 16:18:07 2017 ------##

Number of used cores has changed to 3

in order to avoid CPU overloading.

Report pages and figures are being generated for the c2 collection ...

   Heat maps are being generated for top-ranked gene sets 

based on logFC ... 

   Summary plots are being generated ... 

   Comparison summary plots are being generated  ...

   There are more than 2 contrasts!

Report pages and figures are being generated for the c5BP collection ...

   GO graphs are being generated for top-ranked GO terms

based on med.rank ... 


Building most specific GOs .....

( 10418 GO terms found. )


Build GO DAG topology ..........


 There are no adj nodes for node: GO:0061857

Error in switch(type, isa = 0, partof = 1, -1) : 

  EXPR must be a length 1 vector

In addition: There were 50 or more warnings (use warnings() to see the first 50)

> head(warnings())
Warning messages:
1: In generateMainReport(object, display.top = number, sort.by = sort.by,  ... :
  EGSEA report has been found. Change 'report.dir' to generate a fresh report.

2: In image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks,  ... :
  unsorted 'breaks' will be sorted before use
3: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored
4: In image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks,  ... :
  unsorted 'breaks' will be sorted before use
5: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored
6: In image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks,  ... :
  unsorted 'breaks' will be sorted before use
> tail(warnings())
Warning messages:
1: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored
2: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored
3: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored
4: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored
5: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored
6: In write.csv(csv.out, file = paste0(file.name, ".csv"),  ... :
  attempt to set 'col.names' ignored

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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  
[9] base     

other attached packages:
 [1] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0  EGSEA_1.6.0         
 [4] pathview_1.18.0      topGO_2.30.0         SparseM_1.77        
 [7] GO.db_3.5.0          graph_1.56.0         gage_2.28.0         
[10] EGSEAdata_1.6.0      org.Hs.eg.db_3.5.0   AnnotationDbi_1.40.0
[13] IRanges_2.12.0       S4Vectors_0.16.0     Biobase_2.38.0      
[16] BiocGenerics_0.24.0  edgeR_3.20.1         limma_3.34.1        

loaded via a namespace (and not attached):
 [1] nlme_3.1-131             bitops_1.0-6             matrixStats_0.52.2      
 [4] GSVA_1.26.0              R2HTML_2.3.2             bit64_0.9-7             
 [7] RColorBrewer_1.1-2       httr_1.3.1               Rgraphviz_2.22.0        
[10] tools_3.4.2              doRNG_1.6.6              R6_2.2.2                
[13] DT_0.2                   KernSmooth_2.23-15       DBI_0.7                 
[16] lazyeval_0.2.1           colorspace_1.3-2         bit_1.1-12              
[19] compiler_3.4.2           plotly_4.7.1             pkgmaker_0.22           
[22] labeling_0.3             caTools_1.17.1           KEGGgraph_1.38.1        
[25] scales_0.5.0             PADOG_1.20.0             stringr_1.2.0           
[28] digest_0.6.12            XVector_0.18.0           pkgconfig_2.0.1         
[31] htmltools_0.3.6          HTMLUtils_0.1.7          htmlwidgets_0.9         
[34] rlang_0.1.4              RSQLite_2.0              shiny_1.0.5             
[37] bindr_0.1                hwriter_1.3.2            jsonlite_1.5            
[40] gtools_3.5.0             dplyr_0.7.4              RCurl_1.95-4.8          
[43] magrittr_1.5             GenomeInfoDbData_0.99.1  KEGG.db_3.2.3           
[46] Matrix_1.2-12            Rcpp_0.12.14             munsell_0.4.3           
[49] stringi_1.1.6            yaml_2.1.14              zlibbioc_1.24.0         
[52] globaltest_5.32.0        gplots_3.0.1             KEGGdzPathwaysGEO_1.16.0
[55] plyr_1.8.4               grid_3.4.2               blob_1.1.0              
[58] gdata_2.18.0             lattice_0.20-35          splines_3.4.2           
[61] Biostrings_2.46.0        annotate_1.56.1          KEGGREST_1.18.0         
[64] locfit_1.5-9.1           hgu133plus2.db_3.2.3     hgu133a.db_3.2.3        
[67] rngtools_1.2.4           geneplotter_1.56.0       codetools_0.2-15        
[70] glue_1.2.0               XML_3.98-1.9             GSA_1.03                
[73] metap_0.8                data.table_1.10.4-3      Glimma_1.6.0            
[76] png_0.1-7                httpuv_1.3.5             foreach_1.4.3           
[79] org.Mm.eg.db_3.5.0       tidyr_0.7.2              purrr_0.2.4             
[82] gtable_0.2.0             assertthat_0.2.0         org.Rn.eg.db_3.5.0      
[85] ggplot2_2.2.1            mime_0.5                 xtable_1.8-2            
[88] viridisLite_0.2.0        survival_2.41-3          tibble_1.3.4            
[91] shinythemes_1.1.1        iterators_1.0.8          safe_3.18.0             
[94] registry_0.3             memoise_1.1.0            bindrcpp_0.2            
[97] GSEABase_1.40.1    

 

Thanks,

Jenny

egsea egsea123 • 810 views
ADD COMMENTlink modified 22 months ago by Monther Alhamdoosh40 • written 22 months ago by Jenny Drnevich1.9k

Update: I tried running the example mouse data in the EGSEA123 workflow and had the same error right at the Build GO DAG topology step:

> generateReport(gsa, number = 20, report.dir="./")

EGSEA HTML report is being generated ...

##------ Thu Nov 30 16:29:59 2017 ------##

Number of used cores has changed to 3

in order to avoid CPU overloading.

Report pages and figures are being generated for the c2 collection ...

   Heat maps are being generated for top-ranked gene sets 

based on logFC ... 

   Summary plots are being generated ... 

   Comparison summary plots are being generated  ...

   There are more than 2 contrasts!

Report pages and figures are being generated for the c5BP collection ...

   GO graphs are being generated for top-ranked GO terms

based on med.rank ... 


Building most specific GOs .....

Loading required package: org.Mm.eg.db

( 10665 GO terms found. )


Build GO DAG topology ..........


 There are no adj nodes for node: GO:0061857

Error in switch(type, isa = 0, partof = 1, -1) : 

  EXPR must be a length 1 vector

In addition: There were 50 or more warnings (use warnings() to see the first 50)
ADD REPLYlink written 22 months ago by Jenny Drnevich1.9k
Answer: EGSEA generateReport() error "no adj nodes"
0
gravatar for Monther Alhamdoosh
22 months ago by
Australia/Melbourne/CSL Limited
Monther Alhamdoosh40 wrote:

Hi Jenny, 

Thanks for raising this issue. Apparently, the error is caused by the topGO package that we use to generate the GO graphs. I just re-run the code on Mac and Linux and it worked without any errors. It seems topGO fails under Windows for the functions we use. I haven't tested that yet. I will do later today when I get access to a Windows machine. 

topGO seems to fail at after running this part of the code: 

library(EGSEAdata)

data("il13.data")

mappingDB = "org.Hs.eg.db"

gl = rep(0, length(rownames(il13.data$voom$E)))

names(gl) = rownames(il13.data$voom$E)

topDiffGenes <- function (allScore) {
    return(allScore < 0.01)
}

topGOdataBP <- new("topGOdata",ontology = "BP", allGenes = gl, geneSel = topDiffGenes, nodeSize = 10, annot = annFUN.org, mapping=mappingDB)

The warnings are due to misuse of write.csv. We will fix shortly. Thanks for reporting it :) 

Cheers,

Monther

ADD COMMENTlink written 22 months ago by Monther Alhamdoosh40
Thanks! Please let me know when the bug is fixed. Jenny From: Monther Alhamdoosh [bioc] [mailto:noreply@bioconductor.org] Sent: Thursday, November 30, 2017 7:01 PM To: Zadeh, Jenny Drnevich <drnevich@illinois.edu> Subject: [bioc] A: EGSEA generateReport() error "no adj nodes" Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Monther Alhamdoosh<https: support.bioconductor.org="" u="" 10001=""/> wrote Answer: EGSEA generateReport() error "no adj nodes"<https: support.bioconductor.org="" p="" 103640="" #103642="">: Hi Jenny, Thanks for raising this issue. Apparently, the error is caused by the topGO package that we use to generate the GO graphs. I just re-run the code on Mac and Linux and it worked without any errors. It seems topGO fails under Windows for the functions we use. I haven't tested that yet. I will do later today when I get access to a Windows machine. topGO seems to fail at after running this part of the code: library(EGSEAdata) data("il13.data") mappingDB = "org.Hs.eg.db" gl = rep(0, length(rownames(il13.data$voom$E))) names(gl) = rownames(il13.data$voom$E) topDiffGenes <- function (allScore) { return(allScore < 0.01) } topGOdataBP <- new("topGOdata",ontology = "BP", allGenes = gl, geneSel = topDiffGenes, nodeSize = 10, annot = annFUN.org, mapping=mappingDB) The warnings are due to misuse of write.csv. We will fix shortly. Thanks for reporting it :) Cheers, Monther ________________________________ Post tags: EGSEA, EGSEA123 You may reply via email or visit A: EGSEA generateReport() error "no adj nodes"
ADD REPLYlink written 22 months ago by Jenny Drnevich1.9k
Answer: EGSEA generateReport() error "no adj nodes"
0
gravatar for Monther Alhamdoosh
22 months ago by
Australia/Melbourne/CSL Limited
Monther Alhamdoosh40 wrote:

Hi Jenny, 

I just tested the workflow code on Windows and it ran without any errors. You may consider updating your Bioconductor packages to the latest versions before running EGSEA. This could solve the problem. 

You can update your packages with

library(BiocInstaller)

biocLite()

Can you please try and let me know how you go? 

Anyway, I just pushed a new version to the Release branch where I added a tryCatch to go around this error in case it happened again. It should build soon and appear with EGSEA 1.6.1

Thanks,

Monther

ADD COMMENTlink written 22 months ago by Monther Alhamdoosh40

Hi Monther,

I had updated all my packages in the last week or two, but I went ahead and updated again today but still had the same error with EGSEA 1.6.0. The new version hasn’t been pushed through yet, but I’ll check again tomorrow. Thanks for getting a workaround done so fast! It is weird that you were able to run the workflow code on a Windows machine but I was not. I'll see if I can get one of my co-workers to try to replicate my problem. My sessionInfo is below.

Thanks,

Jenny

> generateReport(gsa, number = 20, report.dir="EGSEAtest/")

EGSEA HTML report is being generated ...
...
Building most specific GOs .....

Loading required package: org.Mm.eg.db

( 10665 GO terms found. )


Build GO DAG topology ..........


 There are no adj nodes for node: GO:0061857

Error in switch(type, isa = 0, partof = 1, -1) : 

  EXPR must be a length 1 vector

In addition: There were 50 or more warnings (use warnings() to see the first 50)

> sessionInfo()

R version 3.4.2 (2017-09-28)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows >= 8 x64 (build 9200)


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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:

 [1] org.Mm.eg.db_3.5.0   EGSEA_1.6.0          pathview_1.18.0      org.Hs.eg.db_3.5.0  

 [5] topGO_2.30.0         SparseM_1.77         GO.db_3.5.0          graph_1.56.0        

 [9] AnnotationDbi_1.40.0 IRanges_2.12.0       S4Vectors_0.16.0     gage_2.28.0         

[13] Biobase_2.38.0       BiocGenerics_0.24.0  EGSEAdata_1.6.0      edgeR_3.20.1        

[17] limma_3.34.2         BiocInstaller_1.28.0


loaded via a namespace (and not attached):

 [1] nlme_3.1-131             bitops_1.0-6             matrixStats_0.52.2      

 [4] GSVA_1.26.0              R2HTML_2.3.2             bit64_0.9-7             

 [7] RColorBrewer_1.1-2       httr_1.3.1               Rgraphviz_2.22.0        

[10] tools_3.4.2              doRNG_1.6.6              R6_2.2.2                

[13] DT_0.2                   KernSmooth_2.23-15       DBI_0.7                 

[16] lazyeval_0.2.1           colorspace_1.3-2         bit_1.1-12              

[19] compiler_3.4.2           plotly_4.7.1             pkgmaker_0.22           

[22] labeling_0.3             caTools_1.17.1           KEGGgraph_1.38.1        

[25] scales_0.5.0             PADOG_1.20.0             stringr_1.2.0           

[28] digest_0.6.12            XVector_0.18.0           pkgconfig_2.0.1         

[31] htmltools_0.3.6          HTMLUtils_0.1.7          htmlwidgets_0.9         

[34] rlang_0.1.4              RSQLite_2.0              shiny_1.0.5             

[37] bindr_0.1                hwriter_1.3.2            jsonlite_1.5            

[40] gtools_3.5.0             dplyr_0.7.4              RCurl_1.95-4.8          

[43] magrittr_1.5             KEGG.db_3.2.3            Matrix_1.2-12           

[46] Rcpp_0.12.14             munsell_0.4.3            stringi_1.1.6           

[49] yaml_2.1.15              zlibbioc_1.24.0          globaltest_5.32.0       

[52] gplots_3.0.1             KEGGdzPathwaysGEO_1.16.0 plyr_1.8.4              

[55] grid_3.4.2               blob_1.1.0               gdata_2.18.0            

[58] lattice_0.20-35          splines_3.4.2            Biostrings_2.46.0       

[61] annotate_1.56.1          KEGGREST_1.18.0          locfit_1.5-9.1          

[64] hgu133plus2.db_3.2.3     hgu133a.db_3.2.3         rngtools_1.2.4          

[67] geneplotter_1.56.0       codetools_0.2-15         glue_1.2.0              

[70] XML_3.98-1.9             GSA_1.03                 metap_0.8               

[73] data.table_1.10.4-3      Glimma_1.6.0             png_0.1-7               

[76] httpuv_1.3.5             foreach_1.4.3            tidyr_0.7.2             

[79] purrr_0.2.4              gtable_0.2.0             assertthat_0.2.0        

[82] org.Rn.eg.db_3.5.0       ggplot2_2.2.1            mime_0.5                

[85] xtable_1.8-2             viridisLite_0.2.0        survival_2.41-3         

[88] tibble_1.3.4             shinythemes_1.1.1        iterators_1.0.8         

[91] safe_3.18.0              registry_0.5             memoise_1.1.0           

[94] bindrcpp_0.2             statmod_1.4.30           GSEABase_1.40.1    
ADD REPLYlink written 22 months ago by Jenny Drnevich1.9k
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