Brian Smith
2015-Dec-07 20:34 UTC
[R] ChAMP: champ.runCombat error with methylation 450k data
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]]
Bert Gunter
2015-Dec-07 20:40 UTC
[R] ChAMP: champ.runCombat error with methylation 450k data
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]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.