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

[Bert Gunter]

Champ is a BioConductor package. You should post to the Bioconductor
Help, not here.

Cheers,
Bert


Bert Gunter

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
   -- Clifford Stoll


On Mon, Dec 7, 2015 at 12:34 PM, Brian Smith <bsmith030465 at gmail.com> wrote:
> 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
>
>         [[alternative HTML version deleted]]
>
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