kasperdanielhansen
commented
7 years ago Yes.
You're trying to use reference data from EPIC arrays which is not available. Instead, use convertArray()to convert your data to look like 450k data and then run the function.
Hi, I was trying to use minfi to estimate cell counts for illumina EPIC data. I upgraded both R and bioconductor, but couldn't execute estimateCellCounts because package "FlowSorted.Blood.EPIC" couldn't be loaded. Am I doing something wrong?
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
[10] base
other attached packages: [1] FlowSorted.Blood.450k_1.12.0 gap_1.1-16
[3] som_0.3-5.1 pvclust_2.0-0
[5] reshape_0.8.6 data.table_1.10.2
[7] foreign_0.8-67 preprocessCore_1.36.0
[9] gtools_3.5.0 RnBeads_1.6.1
[11] plyr_1.8.4 methylumi_2.20.0
[13] minfi_1.20.2 bumphunter_1.14.0
[15] locfit_1.5-9.1 iterators_1.0.8
[17] foreach_1.4.3 Biostrings_2.42.1
[19] XVector_0.14.0 SummarizedExperiment_1.4.0
[21] FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.4.0
[23] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.26.2
[25] AnnotationDbi_1.36.2 reshape2_1.4.2
[27] scales_0.4.1 Biobase_2.34.0
[29] illuminaio_0.16.0 matrixStats_0.51.0
[31] limma_3.30.9 gridExtra_2.2.1
[33] gplots_3.0.1 ggplot2_2.2.1
[35] fields_8.10 maps_3.1.1
[37] spam_1.4-0 ff_2.2-13
[39] bit_1.1-12 cluster_2.0.5
[41] RColorBrewer_1.1-2 MASS_7.3-45
[43] GenomicRanges_1.26.2 GenomeInfoDb_1.10.2
[45] IRanges_2.8.1 S4Vectors_0.12.1
[47] BiocGenerics_0.20.0 BiocInstaller_1.24.0
loaded via a namespace (and not attached): [1] nlme_3.1-130 bitops_1.0-6 httr_1.2.1
[4] tools_3.3.2 doRNG_1.6 nor1mix_1.2-2
[7] R6_2.2.0 KernSmooth_2.23-15 DBI_0.5-1
[10] lazyeval_0.2.0 colorspace_1.3-2 base64_2.0
[13] pkgmaker_0.22 rtracklayer_1.34.1 caTools_1.17.1
[16] genefilter_1.56.0 quadprog_1.5-5 stringr_1.1.0
[19] digest_0.6.12 Rsamtools_1.26.1 siggenes_1.48.0
[22] GEOquery_2.40.0 RSQLite_1.1-2 mclust_5.2.2
[25] BiocParallel_1.8.1 RCurl_1.95-4.8 magrittr_1.5
[28] Matrix_1.2-8 Rcpp_0.12.9 munsell_0.4.3
[31] stringi_1.1.2 zlibbioc_1.20.0 gdata_2.17.0
[34] lattice_0.20-34 splines_3.3.2 multtest_2.30.0
[37] annotate_1.52.1 beanplot_1.2 rngtools_1.2.4
[40] codetools_0.2-15 biomaRt_2.30.0 XML_3.98-1.5
[43] gtable_0.2.0 openssl_0.9.6 assertthat_0.1
[46] xtable_1.8-2 survival_2.40-1 tibble_1.2
[49] GenomicAlignments_1.10.0 registry_0.3 memoise_1.0.0