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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