error in champ.DMR using DMRcate (v2.8.3)
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Entering edit mode
mia • 0
@mia-13303
Last seen 4.1 years ago

I got the following error when running champ.DMR with DMRcate as the method. The package "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" was installed successfully and can be loaded without problem. Can anyone help me resolve this? Thanks.

> res.DMRcate=champ.DMR(beta=BetaVal,
+                 pheno=disease,
+                 arraytype="450K",
+                 method = "DMRcate",
+                 minProbes=3,
+                 adjPvalDmr=0.05,
+                 cores=1,
+                 rmSNPCH=F,
+                 fdr=0.05,
+                 mafcut=0.05,
+                 lambda=1000,
+                 C=2)
[===========================]
[<<<<< ChAMP.DMR START >>>>>]
-----------------------------
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
1 cores will be used to do parallel DMRcate computing.
<< Find DMR with DMRcate Method >>
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Error in get(ann) : 
  object 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19' not found
Calls: champ.DMR ... cpg.annotate -> makeGenomicRatioSetFromMatrix -> get -> get
Execution halted
champ dmrcate IlluminaHumanMethylationEPICanno.ilm10b2.hg19 • 805 views
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Entering edit mode
mia • 0
@mia-13303
Last seen 4.1 years ago
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

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

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

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
 [2] lmf_1.2                                            
 [3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
 [4] ChAMP_2.8.3                                        
 [5] IlluminaHumanMethylationEPICmanifest_0.3.0         
 [6] Illumina450ProbeVariants.db_1.12.0                 
 [7] DMRcate_1.12.1                                     
 [8] DMRcatedata_1.10.1                                 
 [9] DSS_2.14.0                                         
[10] bsseq_1.10.0                                       
[11] FEM_3.4.0                                          
[12] graph_1.52.0                                       
[13] org.Hs.eg.db_3.4.1                                 
[14] impute_1.50.1                                      
[15] igraph_0.7.1                                       
[16] corrplot_0.73                                      
[17] marray_1.54.0                                      
[18] limma_3.32.2                                       
[19] Matrix_1.1-4                                       
[20] AnnotationDbi_1.38.1                               
[21] ChAMPdata_2.8.1                                    
[22] minfi_1.22.1                                       
[23] bumphunter_1.16.0                                  
[24] locfit_1.5-9.1                                     
[25] Biostrings_2.44.1                                  
[26] XVector_0.16.0                                     
[27] SummarizedExperiment_1.6.3                         
[28] DelayedArray_0.2.7                                 
[29] Biobase_2.34.0                                     
[30] GenomicRanges_1.28.3                               
[31] GenomeInfoDb_1.12.2                                
[32] IRanges_2.10.2                                     
[33] S4Vectors_0.14.3                                   
[34] BiocGenerics_0.22.0                                
[35] dendextend_1.5.2                                   
[36] magrittr_1.5                                       
[37] data.table_1.10.4                                  
[38] ggplot2_2.2.1                                      
[39] doParallel_1.0.10                                  
[40] iterators_1.0.7                                    
[41] foreach_1.4.2                                      
[42] RSQLite_1.1-2                                      
[43] Rcpp_0.12.11                                       
[44] RPMM_1.25                                          
[45] cluster_1.15.3                                     
[46] shiny_1.0.3                                        
[47] mime_0.5                                           
[48] httpuv_1.3.3                                       
[49] matrixStats_0.52.2                                 
[50] digest_0.6.12                                      
[51] R.utils_2.5.0                                      
[52] R.oo_1.21.0                                        
[53] R.methodsS3_1.7.1                                  
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Entering edit mode
Yuan Tian ▴ 90
@yuan-tian-9598
Last seen 18 months ago

Hello Mia:

I just tested DMRcate function on a EPIC data on my computer, it seems works fine. Below is my code:

​> myDMR <- champ.DMR(myFilter$beta,pheno=myFilter$pd$Sample_Group,method="DMRcate",arraytype="EPIC")
[===========================]
[<<<<< ChAMP.DMR START >>>>>]
-----------------------------
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
3 cores will be used to do parallel DMRcate computing.
<< Find DMR with DMRcate Method >>
Your contrast returned 246813 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Fitting chr1...
Fitting chr10...
Fitting chr11...
Fitting chr13...
Fitting chr14...
Fitting chr16...
Fitting chr12...
Fitting chr17...
Fitting chr19...
Fitting chr15...
Fitting chr2...
Fitting chr21...
Fitting chr18...
Fitting chr4...
Fitting chr20...
Fitting chr7...
Fitting chr3...
Fitting chr22...
Fitting chr5...
Fitting chr6...
Fitting chr8...
Fitting chr9...

 

And seems your sessionInfo() is also correct. That's wired...Could you try directly load IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package, and see if you can find object IlluminaHumanMethylationEPICanno.ilm10b2.hg19 in your R?

 

Best

Yuan Tian

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Entering edit mode

Hi Yuan,

Thanks for your reply.

 

I just tried to load IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package directly and it worked fine. But, when I tried to find the object using get("IlluminaHumanMethylationEPICanno.ilm10b2.hg19"), the same error came out saying that object 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19' not found.

 

One thing I'd like to mention is that I got the error when running on HPC server (Linux). And everything worked fine on my laptop, where the same versions of R and ChAMP were installed.

 

Another thing I feel a little confused is that in the function I specified my array type to be "450K" and it seems that the annotation package for 450K was loaded successfully. I wasn't sure why it also loaded annotation package for EPIC array.

 

Thanks for your help!

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