Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
2
0
Entering edit mode
erinkello • 0
@erinkello-19342
Last seen 5.9 years ago
University of Pittsburgh

Hello,

I am attempting to perform gene enrichment analysis on methylation data. The program can not find the EPIC annotation file. To be sure it was there I downloaded this file using the below command. Following this I received the same error. Could anyone help with this?

 if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b2.hg19", version = "3.8")

My code:

 myGSEAexp <- champ.GSEA(beta=myNorm, DMP=myDMP[[1]], DMR=DMREX, arraytype="EPIC",adjPval=0.05, method="gometh")
[===========================]
[<<<< ChAMP.GSEA START >>>>>]
-----------------------------
<< Prepare CpG List Ready  >>
  Calculating GSEA with gometh method on DMP CpG list
  Note that gometh method would count numbers of CpGs in each genes and correct this bias.
Error in getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) : 
  object 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19' not found
> 


Session info

R version 3.5.0 (2018-04-23)
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 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
 [3] bindrcpp_0.2.2                                     
 [4] shiny_1.2.0                                        
 [5] ChAMP_2.12.2                                       
 [6] IlluminaHumanMethylationEPICmanifest_0.3.0         
 [7] Illumina450ProbeVariants.db_1.18.0                 
 [8] DMRcate_1.18.0                                     
 [9] DMRcatedata_1.18.0                                 
[10] DSS_2.30.1                                         
[11] bsseq_1.18.0                                       
[12] FEM_3.10.0                                         
[13] graph_1.60.0                                       
[14] org.Hs.eg.db_3.7.0                                 
[15] impute_1.56.0                                      
[16] igraph_1.2.2                                       
[17] corrplot_0.84                                      
[18] marray_1.60.0                                      
[19] limma_3.38.3                                       
[20] Matrix_1.2-14                                      
[21] AnnotationDbi_1.44.0                               
[22] ChAMPdata_2.14.0                                   
[23] minfi_1.28.3                                       
[24] bumphunter_1.24.5                                  
[25] locfit_1.5-9.1                                     
[26] iterators_1.0.10                                   
[27] foreach_1.4.4                                      
[28] Biostrings_2.50.2                                  
[29] XVector_0.22.0                                     
[30] SummarizedExperiment_1.12.0                        
[31] DelayedArray_0.8.0                                 
[32] BiocParallel_1.16.5                                
[33] matrixStats_0.54.0                                 
[34] Biobase_2.42.0                                     
[35] GenomicRanges_1.34.0                               
[36] GenomeInfoDb_1.18.1                                
[37] IRanges_2.16.0                                     
[38] S4Vectors_0.20.1                                   
[39] BiocGenerics_0.28.0                                
[40] dplyr_0.7.8                                        

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'data.table' is missing or broken
2: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'checkmate' is missing or broken
3: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'rlang' is missing or broken
4: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'VariantAnnotation' is missing or broken
5: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'colorspace' is missing or broken
6: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'tibble' is missing or broken
7: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'curl' is missing or broken
8: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'openssl' is missing or broken
> 
champ bioconductor methyaltion epic array • 2.1k views
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1
Entering edit mode
@lluis-revilla-sancho
Last seen 10 hours ago
European Union

Install the package: "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" and see if it happens again

ADD COMMENT
0
Entering edit mode

Ok, thank you. I have the correct file now. I can see the file in the packages i have loaded, however i am still getting the same error as above. I checked the dependencies and all are installed as well. Is there an obvious error that i'm missing?

ADD REPLY
1
Entering edit mode

Could you update all the other packages reported at the end of the R session? (curl, colorspace, tibble, openssl, VariantAnnotation, data.table, checkmate and rlang). Also these errors appearing after the R session information means you have some problems in the installation: do you have all the packages in the same folder and just once? (check the folders .libPaths())

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0
Entering edit mode

Useful to confirm that at least the Bioconductor packages are consistent, using BiocManager::valid().

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0
Entering edit mode
erinkello • 0
@erinkello-19342
Last seen 5.9 years ago
University of Pittsburgh

Thank you for the help! I updated my packages and checked that my packages were in the correct directory. I then used the require(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) when loading the champ library. It seems like for some reason this was not being loaded with the other packages. This fixed the problem and the command is now working.

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