[R] ChAMP: champ.runCombat error with methylation 450k data

[Brian Smith]

Hi,

I was trying to run COMBAT on methylation data, but keep on getting an
error:

Error in while (change > conv) { : missing value where TRUE/FALSE needed

The error occurs irrespective of whether I give the entire or reduced
(variation filter keeps only about 140k CpGs) datasets.

Is there any other preprocessing that I should be doing?

thanks!!

my code and sessionInfo():



> betacombat <- champ.runCombat(beta.c = beta3, pd = ss, logitTrans = TRUE)
Preparing files for ComBat
Zeros in your dataset have been replaced with 0.000001
Your data is being logit transformed before batch correction
Beginning batch correction
Found 60 batches
Found 0  categorical covariate(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Error in while (change > conv) { : missing value where TRUE/FALSE needed
> traceback()
3: it.sol(s.data[, batches[[i]]], gamma.hat[i, ], delta.hat[i, ],
       gamma.bar[i], t2[i], a.prior[i], b.prior[i])
2: champ.ComBat(dat = log, batch = batch, mod = mod, par.prior = TRUE)
1: champ.runCombat(beta.c = betaASDnorm3, pd = ss_2ASD, logitTrans = TRUE)
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

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   base

other attached packages:
 [1] ChAMP_1.8.0
 Illumina450ProbeVariants.db_1.6.0
 [3] ChAMPdata_1.8.0
 IlluminaHumanMethylation450kmanifest_0.4.0
 [5] biomaRt_2.26.1                             data.table_1.9.6

 [7] foreign_0.8-65                             preprocessCore_1.32.0

 [9] gtools_3.5.0                               BiocInstaller_1.20.1

[11] ggdendro_0.1-17                            reshape_0.8.5

[13] RnBeads_1.2.0                              plyr_1.8.3

[15] methylumi_2.16.0                           minfi_1.16.0

[17] bumphunter_1.10.0                          locfit_1.5-9.1

[19] iterators_1.0.8                            foreach_1.4.3

[21] Biostrings_2.38.2                          XVector_0.10.0

[23] SummarizedExperiment_1.0.1                 lattice_0.20-33

[25] FDb.InfiniumMethylation.hg19_2.2.0         org.Hs.eg.db_3.2.3

[27] RSQLite_1.0.0                              DBI_0.3.1

[29] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2    GenomicFeatures_1.22.5

[31] AnnotationDbi_1.32.0                       reshape2_1.4.1

[33] scales_0.3.0                               Biobase_2.30.0

[35] illuminaio_0.12.0                          matrixStats_0.15.0

[37] limma_3.26.3                               gridExtra_2.0.0

[39] gplots_2.17.0                              ggplot2_1.0.1

[41] fields_8.3-5                               maps_3.0.0-2

[43] spam_1.3-0                                 ff_2.2-13

[45] bit_1.1-12                                 cluster_2.0.3

[47] RColorBrewer_1.1-2                         MASS_7.3-43

[49] GenomicRanges_1.22.1                       GenomeInfoDb_1.6.1

[51] IRanges_2.4.4                              S4Vectors_0.8.3

[53] BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] nlme_3.1-121            bitops_1.0-6            tools_3.2.2
  doRNG_1.6
 [5] nor1mix_1.2-1           KernSmooth_2.23-15      mgcv_1.8-7
 colorspace_1.2-6
 [9] DNAcopy_1.44.0          base64_1.1              chron_2.3-47
 wateRmelon_1.10.0
[13] RPMM_1.20               pkgmaker_0.22           labeling_0.3
 rtracklayer_1.30.1
[17] caTools_1.17.1          genefilter_1.52.0       quadprog_1.5-5
 stringr_1.0.0
[21] digest_0.6.8            Rsamtools_1.22.0        siggenes_1.44.0
  GEOquery_2.36.0
[25] impute_1.44.0           mclust_5.1              BiocParallel_1.4.0
 RCurl_1.95-4.7
[29] magrittr_1.5            Matrix_1.2-2            futile.logger_1.4.1
  Rcpp_0.12.2
[33] munsell_0.4.2           proto_0.3-10            stringi_1.0-1
  zlibbioc_1.16.0
[37] gdata_2.17.0            splines_3.2.2           multtest_2.26.0
  annotate_1.48.0
[41] beanplot_1.2            igraph_1.0.1            corpcor_1.6.8
  rngtools_1.2.4
[45] marray_1.48.0           codetools_0.2-14        mixOmics_5.2.0
 futile.options_1.0.0
[49] XML_3.98-1.3            lambda.r_1.1.7          gtable_0.1.2
 xtable_1.8-0
[53] survival_2.38-3         ellipse_0.3-8
GenomicAlignments_1.6.1 registry_0.3
[57] sva_3.18.0              rgl_0.95.1201

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