Entering edit mode
I'm trying to use minfi's readGEORawFile function to read in methylation data from the GEO series GSE59091, but I keep getting the following error:
file<-"GSE59091_unmethylated_methylated_cor.txt" GEO<-readGEORawFile(file,sep=" ",Uname="Unmethylated.signal", + Mname="Methylated.signal") Read 485512 rows and 391 (of 586) columns from 1.054 GB file in 00:00:16 Error in FUN(X[[i]], ...) : assay colnames() must be NULL or equal colData rownames()
sessionInfo:
R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin15.5.0 (64-bit) Running under: OS X 10.11.6 (El Capitan) 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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [2] GEOquery_2.39.3 [3] RColorBrewer_1.1-2 [4] IlluminaHumanMethylationEPICmanifest_0.3.0 [5] IlluminaHumanMethylation450kmanifest_0.4.0 [6] minfi_1.19.14 [7] bumphunter_1.13.1 [8] locfit_1.5-9.1 [9] iterators_1.0.8 [10] foreach_1.4.3 [11] Biostrings_2.41.4 [12] XVector_0.13.7 [13] SummarizedExperiment_1.3.82 [14] GenomicRanges_1.25.94 [15] GenomeInfoDb_1.9.12 [16] IRanges_2.7.15 [17] S4Vectors_0.11.14 [18] lattice_0.20-34 [19] Biobase_2.33.3 [20] BiocGenerics_0.19.2 [21] BiocInstaller_1.23.9 loaded via a namespace (and not attached): [1] mclust_5.2 base64_2.0 Rcpp_0.12.7 [4] Rsamtools_1.25.2 digest_0.6.10 R6_2.1.3 [7] plyr_1.8.4 chron_2.3-47 RSQLite_1.0.0 [10] httr_1.2.1 zlibbioc_1.19.0 GenomicFeatures_1.25.16 [13] data.table_1.9.6 annotate_1.51.0 Matrix_1.2-7.1 [16] preprocessCore_1.35.0 splines_3.3.1 BiocParallel_1.7.8 [19] stringr_1.1.0 RCurl_1.95-4.8 biomaRt_2.29.2 [22] rtracklayer_1.33.12 multtest_2.29.0 pkgmaker_0.22 [25] openssl_0.9.4 quadprog_1.5-5 codetools_0.2-14 [28] matrixStats_0.50.2 XML_3.98-1.4 reshape_0.8.5 [31] GenomicAlignments_1.9.6 MASS_7.3-45 bitops_1.0-6 [34] grid_3.3.1 nlme_3.1-128 xtable_1.8-2 [37] registry_0.3 DBI_0.5-1 magrittr_1.5 [40] stringi_1.1.1 genefilter_1.55.2 doRNG_1.6 [43] limma_3.29.21 nor1mix_1.2-2 siggenes_1.47.0 [46] tools_3.3.1 illuminaio_0.15.1 rngtools_1.2.4 [49] survival_2.39-5 AnnotationDbi_1.35.4 beanplot_1.2