RnBeads - error with 'rnb.run.differential' module
2
0
Entering edit mode
Brian Smith ▴ 120
@brian-smith-6197
Last seen 10 months ago
United States

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 

RnBeads illimina 450k methylation • 1.2k views
ADD COMMENT
0
Entering edit mode
pavlo.lutsik ▴ 10
@pavlolutsik-9032
Last seen 5.7 years ago
Germany

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 COMMENT
0
Entering edit mode
Brian Smith ▴ 120
@brian-smith-6197
Last seen 10 months ago
United States

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 COMMENT

Login before adding your answer.

Traffic: 651 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6