Question: RnBeads - error with 'rnb.run.differential' module
0
gravatar for Brian Smith
4.0 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

Hi,

I was trying to run the ‘rnb.run.differential’ module, but get an error. My rnb.options, test data, the error, traceback and sessionInfo are below. Thanks for any pointers/help!!

 

#####
#### my options
#####
> rnb.options("covariate.adjustment.columns"=c("AGE"))
> rnb.options(differential.site.test.method="refFreeEWAS")
> rnb.options("differential.comparison.columns”=“phenotype”)


#####
## Datasets
#####
> rnb.set.norm <- rnb.execute.normalization(rnb.set4, method="swan",
                                          bgcorr.method="methylumi.noob")

## test data with ~ 3k cogs
> rnb.test2 <- rnb.execute.variability.removal(rnb.set.norm, 0.13)$dataset

> rnb.test2

Object of class RnBeadRawSet
      43 samples
    3019 probes
    of which: 3019 CpG, 0 CpH, and 0 rs
Region types:
        2673 regions of type tiling
        1801 regions of type genes
         605 regions of type promoters
         363 regions of type cpgislands
Intensity information is present
Detection p-values are present
Bead counts are present
Quality control information is present
Summary of normalization procedures:
    The methylation data was normalized with method swan.
    Background correction was performed with method methylumi.noob.


####
## Run
#####

> rnb.run.differential(rnb.set=rnb.test2, dir.reports=report.dir4)
Error in if (any(range.diff == 0)) { : 
  missing value where TRUE/FALSE needed

> traceback()
6: refFreeEWASP(X, inds.g1, inds.g2, adjustment.table = adjustment.table, 
       paired = paired)
5: computeDiffTab.default.site(X, inds.g1 = inds.g1, inds.g2 = inds.g2, 
       diff.method = diff.method, paired = paired, adjustment.table = adjustment.table, 
       eps = eps)
4: computeDiffTab.extended.site(b, inds.g1 = inds.g1, inds.g2 = inds.g2, 
       ...)
3: computeDiffMeth.bin.site(meth(x), inds.g1 = cmp.info.cur$group.inds$group1, 
       inds.g2 = cmp.info.cur$group.inds$group2, covg = covg(x), 
       covg.thres = covg.thres, paired = cmp.info.cur$paired, adjustment.table = cmp.info.cur$adjustment.table, 
       ...)
2: rnb.execute.computeDiffMeth(rnb.set, cmp.cols, region.types = reg.types, 
       n.perm = permutations, covg.thres = rnb.getOption("filtering.coverage.threshold"), 
       pheno.cols.all.pairwise = rnb.getOption("differential.comparison.columns.all.pairwise"), 
       columns.pairs = rnb.getOption("columns.pairing"), columns.adj = rnb.getOption("covariate.adjustment.columns"), 
       adjust.sva = rnb.getOption("differential.adjustment.sva"), 
       pheno.cols.adjust.sva = rnb.getOption("inference.targets.sva"), 
       adjust.celltype = rnb.getOption("differential.adjustment.celltype"), 
       skip.sites = !rnb.getOption("analyze.sites"), disk.dump = disk.dump, 
       disk.dump.dir = disk.dump.dir)
1: rnb.run.differential(rnb.set = rnb.test2, dir.reports = report.dir4)

 

 

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] RefFreeEWAS_1.3                            isva_1.8                                  
 [3] fastICA_1.2-0                              qvalue_2.2.0                              
 [5] RnBeads.hg19_1.2.0                         IlluminaHumanMethylation450kmanifest_0.4.0
 [7] RnBeads_1.2.0                              plyr_1.8.3                                
 [9] methylumi_2.16.0                           minfi_1.16.0                              
[11] bumphunter_1.10.0                          locfit_1.5-9.1                            
[13] iterators_1.0.8                            foreach_1.4.3                             
[15] Biostrings_2.38.0                          XVector_0.10.0                            
[17] SummarizedExperiment_1.0.0                 lattice_0.20-33                           
[19] FDb.InfiniumMethylation.hg19_2.2.0         org.Hs.eg.db_3.2.3                        
[21] RSQLite_1.0.0                              DBI_0.3.1                                 
[23] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2    GenomicFeatures_1.22.0                    
[25] AnnotationDbi_1.32.0                       reshape2_1.4.1                            
[27] scales_0.3.0                               Biobase_2.30.0                            
[29] illuminaio_0.12.0                          matrixStats_0.14.2                        
[31] limma_3.26.0                               gridExtra_2.0.0                           
[33] gplots_2.17.0                              ggplot2_1.0.1                             
[35] fields_8.3-5                               maps_3.0.0-2                              
[37] spam_1.2-1                                 ff_2.2-13                                 
[39] bit_1.1-12                                 cluster_2.0.3                             
[41] RColorBrewer_1.1-2                         MASS_7.3-44                               
[43] GenomicRanges_1.22.0                       GenomeInfoDb_1.6.0                        
[45] IRanges_2.4.1                              S4Vectors_0.8.0                           
[47] BiocGenerics_0.16.0                       

loaded via a namespace (and not attached):
 [1] nlme_3.1-122            bitops_1.0-6            tools_3.2.2            
 [4] doRNG_1.6               nor1mix_1.2-1           KernSmooth_2.23-15     
 [7] colorspace_1.2-6        base64_1.1              preprocessCore_1.32.0  
[10] pkgmaker_0.22           labeling_0.3            rtracklayer_1.30.1     
[13] caTools_1.17.1          genefilter_1.52.0       quadprog_1.5-5         
[16] stringr_1.0.0           digest_0.6.8            Rsamtools_1.22.0       
[19] siggenes_1.44.0         GEOquery_2.36.0         mclust_5.0.2           
[22] BiocParallel_1.4.0      gtools_3.5.0            RCurl_1.95-4.7         
[25] magrittr_1.5            futile.logger_1.4.1     Rcpp_0.12.1            
[28] munsell_0.4.2           proto_0.3-10            stringi_1.0-1          
[31] zlibbioc_1.16.0         gdata_2.17.0            splines_3.2.2          
[34] multtest_2.26.0         annotate_1.48.0         beanplot_1.2           
[37] igraph_1.0.1            rngtools_1.2.4          codetools_0.2-14       
[40] biomaRt_2.26.0          mixOmics_5.1.2          futile.options_1.0.0   
[43] XML_3.98-1.3            lambda.r_1.1.7          gtable_0.1.2           
[46] reshape_0.8.5           xtable_1.7-4            survival_2.38-3        
[49] pheatmap_1.0.7          ellipse_0.3-8           GenomicAlignments_1.6.1
[52] registry_0.3            rgl_0.95.1367 

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Brian Smith120
Answer: RnBeads - error with 'rnb.run.differential' module
0
gravatar for pavlo.lutsik
4.0 years ago by
pavlo.lutsik10
Germany
pavlo.lutsik10 wrote:

Hi Brian, 

You spotted a bug in the RefFreeEWAS wrapper which was related to missing values in your RnBeadSet object. A fix is already in the RnBeads svn repo.

Thanks for reporting!

Pavlo

 

 

 

ADD COMMENTlink written 4.0 years ago by pavlo.lutsik10
Answer: RnBeads - error with 'rnb.run.differential' module
0
gravatar for Brian Smith
4.0 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

Thanks Pavlo!

So, should I download the package again and re-install?

Also, is there a way to get the test statistics as well (in addition to the p-values that are in the results)?

thanks!! 

ADD COMMENTlink written 4.0 years ago by Brian Smith120
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