Conumee error: Error in .local(query, ref, anno, ...) : query intensities not given for all probes.
This error results when I use
x <- CNV.fit(data[1], controls.data, anno)
The data object was generated by:
rgSet <- combineArrays(rgSet.450k, rgSet.850k) mSet <- preprocessNoob(rgSet, dyeMethod = "single") data <- CNV.load(mSet)
The anno object was made by:
anno <- CNV.create_anno(chrXY = TRUE, exclude_regions = exclude_regions, detail_regions = detail_regions, array_type = "overlap")
Controls data is generated in a similar way to the test data.
Could you please let me what checks to carry out? I current work around this by amending the anno data to reflect the missing problems and end up dropping quite a number of probes in the process.
Many thanks
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 [6] LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] conumee_1.10.0 IlluminaHumanMethylationEPICmanifest_0.3.0 IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 [4] IlluminaHumanMethylation450kmanifest_0.4.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 minfi_1.22.1 [7] bumphunter_1.16.0 locfit_1.5-9.1 iterators_1.0.8 [10] foreach_1.4.3 Biostrings_2.44.1 XVector_0.16.0 [13] SummarizedExperiment_1.6.3 DelayedArray_0.2.7 matrixStats_0.52.2 [16] Biobase_2.36.2 GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 [19] IRanges_2.10.2 S4Vectors_0.14.3 BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] httr_1.2.1 nor1mix_1.2-2 bit64_0.9-7 splines_3.4.0 doRNG_1.6.6 blob_1.1.0 [7] GenomeInfoDbData_0.99.0 Rsamtools_1.28.0 RSQLite_2.0 lattice_0.20-35 limma_3.32.2 quadprog_1.5-5 [13] digest_0.6.12 RColorBrewer_1.1-2 preprocessCore_1.38.1 Matrix_1.2-10 plyr_1.8.4 GEOquery_2.42.0 [19] siggenes_1.50.0 XML_3.98-1.9 biomaRt_2.32.1 genefilter_1.58.1 zlibbioc_1.22.0 xtable_1.8-2 [25] BiocParallel_1.10.1 tibble_1.3.3 openssl_0.9.6 annotate_1.54.0 beanplot_1.2 pkgmaker_0.22 [31] GenomicFeatures_1.28.4 survival_2.41-3 magrittr_1.5 mclust_5.3 memoise_1.1.0 nlme_3.1-131 [37] MASS_7.3-47 tools_3.4.0 registry_0.3 data.table_1.10.4 stringr_1.2.0 rngtools_1.2.4 [43] AnnotationDbi_1.38.1 base64_2.0 compiler_3.4.0 rlang_0.1.1 grid_3.4.0 RCurl_1.95-4.8 [49] bitops_1.0-6 DNAcopy_1.50.1 codetools_0.2-15 multtest_2.32.0 DBI_0.7 reshape_0.8.6 [55] R6_2.2.2 illuminaio_0.18.0 GenomicAlignments_1.12.1 rtracklayer_1.36.3 bit_1.1-12 stringi_1.1.5 [61] Rcpp_0.12.11 |
Thank you for getting back to me. We assumed there was something going on along these lines as I recently had a similar problem with minfi reading in newer EPIC array idats before the update dropped.
Will implement change you recommended.