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supermanrocketboy
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@supermanrocketboy-11690
Last seen 7.1 years ago
I get an error when trying to create my RG set.
library(minfi)
baseDir <- "K:/IDATS"
targets <- read.metharray.sheet(baseDir)
RGSet <- read.metharray.exp(base = baseDir, targets = targets, verbose=T)
Error in read.metharray(files, extended = extended, verbose = verbose, :
The following specified files do not exist:
But no files are listed. Anyone else getting this error?
I created a sample sheet (CSV) and put it in a directory containing all my IDAT files. The sample sheet contains a column called Basename, which has the full file path for each IDAT file (minus the "_Grn.idat" and "_Red.idat" suffix).
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] minfi_1.20.0 bumphunter_1.14.0 [3] locfit_1.5-9.1 iterators_1.0.8 [5] foreach_1.4.3 Biostrings_2.42.0 [7] XVector_0.14.0 SummarizedExperiment_1.4.0 [9] GenomicRanges_1.26.1 GenomeInfoDb_1.8.7 [11] IRanges_2.8.0 S4Vectors_0.12.0 [13] Biobase_2.32.0 BiocGenerics_0.20.0 [15] BiocInstaller_1.24.0 loaded via a namespace (and not attached): [1] mclust_5.2 base64_2.0 Rcpp_0.12.7 [4] lattice_0.20-33 Rsamtools_1.26.1 digest_0.6.10 [7] chron_2.3-47 R6_2.2.0 plyr_1.8.4 [10] RSQLite_1.0.0 httr_1.2.1 zlibbioc_1.20.0 [13] GenomicFeatures_1.26.0 data.table_1.9.6 annotate_1.52.0 [16] Matrix_1.2-7.1 preprocessCore_1.36.0 splines_3.3.1 [19] BiocParallel_1.8.0 stringr_1.1.0 RCurl_1.95-4.8 [22] biomaRt_2.30.0 rtracklayer_1.34.0 multtest_2.30.0 [25] pkgmaker_0.22 openssl_0.9.4 GEOquery_2.40.0 [28] quadprog_1.5-5 codetools_0.2-15 matrixStats_0.51.0 [31] XML_3.98-1.4 reshape_0.8.6 GenomicAlignments_1.10.0 [34] MASS_7.3-45 bitops_1.0-6 grid_3.3.1 [37] nlme_3.1-128 xtable_1.8-2 registry_0.3 [40] DBI_0.5-1 magrittr_1.5 stringi_1.1.2 [43] genefilter_1.56.0 doRNG_1.6 limma_3.30.0 [46] nor1mix_1.2-2 RColorBrewer_1.1-2 siggenes_1.48.0 [49] tools_3.3.1 illuminaio_0.16.0 rngtools_1.2.4 [52] survival_2.39-5 AnnotationDbi_1.36.0 beanplot_1.2
You will need to show the targets file that you are starting with, and probably also what is in K:/IDATS. You might also show what you get if you do
Windows can be sort of weird with network drives, especially if it's a samba mounted linux drive.
Thru extra sleuthing, I found out that I was missing a single "_Red.idat" file for one of my samples.
#problemsolved