The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
0
gravatar for erinkello
4 weeks ago by
erinkello0
University of Pittsburgh
erinkello0 wrote:

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
> 
ADD COMMENTlink modified 22 days ago by godai9876540 • written 4 weeks ago by erinkello0
Answer: C: Error in Champ for Bioconductor performing GSEA analysis on Methlayion array dat
1
gravatar for Lluís Revilla Sancho
29 days ago by
European Union
Lluís Revilla Sancho460 wrote:

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

ADD COMMENTlink written 29 days ago by Lluís Revilla Sancho460

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 REPLYlink written 24 days ago by erinkello0
1

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())

ADD REPLYlink written 23 days ago by Lluís Revilla Sancho460

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

ADD REPLYlink written 23 days ago by Martin Morgan ♦♦ 22k
Answer: Error in Champ for Bioconductor performing GSEA analysis on Methlayion array dat
0
gravatar for erinkello
23 days ago by
erinkello0
University of Pittsburgh
erinkello0 wrote:

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.

ADD COMMENTlink written 23 days ago by erinkello0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 194 users visited in the last hour