bsseq: Failing to reproduce the results
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24 months ago

Hi everyone, I am reproducing my collaborator's bsseq analysis results. But I do not understand what possible reason could be to have different results when our script, threshold input files and package and dependency version (except packages via namespace) is identical?

My collaborator's sessionInfo()

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
  [8] methods   base

other attached packages:
 [1] bsseq_1.22.0                SummarizedExperiment_1.16.0
 [3] DelayedArray_0.12.0         BiocParallel_1.20.0        
 [5] matrixStats_0.55.0          Biobase_2.46.0             
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
 [9] IRanges_2.20.0              S4Vectors_0.24.0           
[11] BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2               compiler_3.6.1           XVector_0.26.0          
 [4] R.methodsS3_1.7.1        bitops_1.0-6             R.utils_2.9.0           
 [7] tools_3.6.1              DelayedMatrixStats_1.8.0 zlibbioc_1.32.0         
[10] rhdf5_2.30.0             lattice_0.20-38          BSgenome_1.54.0         
[13] Matrix_1.2-17            GenomeInfoDbData_1.2.2   rtracklayer_1.46.0      
[16] Biostrings_2.54.0        gtools_3.8.1             locfit_1.5-9.1          
[19] grid_3.6.1               data.table_1.14.2        HDF5Array_1.14.0        
[22] XML_3.98-1.20            limma_3.42.0             Rhdf5lib_1.8.0          
[25] scales_1.0.0             Rsamtools_2.2.0          GenomicAlignments_1.22.0
[28] permute_0.9-5            colorspace_1.4-1         RCurl_1.95-4.12         
[31] munsell_0.5.0            R.oo_1.23.0           

My sessionInfo()

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

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

other attached packages:
 [1] bsseq_1.22.0                SummarizedExperiment_1.16.0
 [3] DelayedArray_0.12.0         BiocParallel_1.20.0        
 [5] matrixStats_0.58.0          Biobase_2.46.0             
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
 [9] IRanges_2.20.0              S4Vectors_0.24.0           
[11] BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6               compiler_3.6.3           XVector_0.26.0          
 [4] R.methodsS3_1.8.1        R.utils_2.10.1           bitops_1.0-7            
 [7] tools_3.6.3              DelayedMatrixStats_1.8.0 zlibbioc_1.32.0         
[10] lifecycle_1.0.0          rhdf5_2.30.0             lattice_0.20-44         
[13] BSgenome_1.54.0          rlang_0.4.11             Matrix_1.3-3            
[16] GenomeInfoDbData_1.2.2   rtracklayer_1.46.0       Biostrings_2.54.0       
[19] gtools_3.8.2             locfit_1.5-9.4           grid_3.6.3              
[22] data.table_1.14.0        R6_2.5.0                 HDF5Array_1.14.0        
[25] XML_3.99-0.3             limma_3.42.0             Rhdf5lib_1.8.0          
[28] GenomicAlignments_1.22.0 scales_1.1.1             Rsamtools_2.2.0         
[31] permute_0.9-5            colorspace_2.0-1         RCurl_1.98-1.3          
[34] munsell_0.5.0            R.oo_1.24.0             
> 

You may find the attached picture for your reference purpose: These are the DMRs we are getting

Would anyone like to share their intuition?

Thank you for your time and consideration.

sequencing EM-seq Differentially Methylated bisulfite DMRs bsseq Regions • 303 views
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