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
