I have recently begun using `minfi` for the analysis of 850K methylation data from the Illumina EPIC array. In following a fairly standard procedure (as in the the 2014 Bioconductor tutorial on using minfi for 450K data), I've encountered the following error, which arises anytime that `mapToGenome` is called:
"Error in out[wh, ] : incorrect number of dimensions"
This is the first time I've used minfi for analyzing EPIC data, but, in all previous instances in which I've used the tool to analyze 450K data, I've never encountered such an error.
Any help in diagnosing and/or resolving this issue would be much appreciated.
Output of traceback():
R > genomeset <- mapToGenome(ratioset_raw)
Error in out[wh, ] : incorrect number of dimensions
R > traceback()
5: getAnnotation(object, what = what, dropNonMapping = TRUE, orderByLocation = orderByLocation,
lociNames = lociNames)
4: getLocations(object, mergeManifest = mergeManifest, orderByLocation = TRUE)
3: .local(object, ...)
2: mapToGenome(ratioset_raw)
1: mapToGenome(ratioset_raw)
Output of biocValid():
* sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.8 (Santiago)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices datasets utils
[8] methods base
other attached packages:
[1] BiocInstaller_1.24.0
[2] nima_0.4.0
[3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[4] IlluminaHumanMethylationEPICmanifest_0.3.0
[5] minfi_1.20.2
[6] bumphunter_1.14.0
[7] locfit_1.5-9.1
[8] iterators_1.0.8
[9] foreach_1.4.3
[10] Biostrings_2.42.1
[11] XVector_0.12.0
[12] SummarizedExperiment_1.2.3
[13] GenomicRanges_1.24.2
[14] GenomeInfoDb_1.10.3
[15] IRanges_2.6.1
[16] S4Vectors_0.12.1
[17] lattice_0.20-34
[18] Biobase_2.34.0
[19] BiocGenerics_0.18.0
[20] here_0.0-5
[21] dtplyr_0.0.1
[22] data.table_1.10.4
[23] dplyr_0.5.0
[24] ggplot2_2.2.1
[25] devtools_1.12.0
[26] colorout_1.1-2
loaded via a namespace (and not attached):
[1] nlme_3.1-131 bitops_1.0-6 matrixStats_0.51.0
[4] RColorBrewer_1.1-2 httr_1.2.1 rprojroot_1.2
[7] tools_3.3.2 backports_1.0.5 doRNG_1.6
[10] nor1mix_1.2-2 R6_2.1.2 DBI_0.4-1
[13] lazyeval_0.2.0 colorspace_1.3-2 withr_1.0.2
[16] gridExtra_2.2.1 base64_2.0 curl_2.3
[19] git2r_0.18.0 preprocessCore_1.36.0 pkgmaker_0.22
[22] rtracklayer_1.34.2 scales_0.4.1 genefilter_1.56.0
[25] quadprog_1.5-5 stringr_1.2.0 digest_0.6.10
[28] Rsamtools_1.26.1 illuminaio_0.16.0 siggenes_1.48.0
[31] GEOquery_2.40.0 limma_3.30.12 ggthemes_3.4.0
[34] RSQLite_1.0.0 mclust_5.2.2 BiocParallel_1.8.1
[37] gtools_3.5.0 RCurl_1.95-4.8 magrittr_1.5
[40] Matrix_1.2-7.1 Rcpp_0.12.8 munsell_0.4.3
[43] stringi_1.1.2 MASS_7.3-45 zlibbioc_1.20.0
[46] plyr_1.8.4 grid_3.3.2 splines_3.3.2
[49] multtest_2.30.0 GenomicFeatures_1.26.3 annotate_1.52.1
[52] beanplot_1.2 rngtools_1.2.4 codetools_0.2-15
[55] biomaRt_2.30.0 XML_3.98-1.5 gtable_0.2.0
[58] openssl_0.9.6 reshape_0.8.6 assertthat_0.1
[61] xtable_1.8-2 survival_2.40-1 tibble_1.2
[64] GenomicAlignments_1.8.4 AnnotationDbi_1.36.2 registry_0.3
[67] memoise_1.0.0
* Out-of-date packages
Package
BiocGenerics "BiocGenerics"
DBI "DBI"
dichromat "dichromat"
digest "digest"
GenomicAlignments "GenomicAlignments"
GenomicRanges "GenomicRanges"
gtools "gtools"
IRanges "IRanges"
labeling "labeling"
locfit "locfit"
munsell "munsell"
R.methodsS3 "R.methodsS3"
R6 "R6"
RColorBrewer "RColorBrewer"
Rcpp "Rcpp"
RSQLite "RSQLite"
LibPath
BiocGenerics "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
DBI "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
dichromat "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
digest "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
GenomicAlignments "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
GenomicRanges "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
gtools "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
IRanges "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
labeling "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
locfit "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
munsell "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
R.methodsS3 "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
R6 "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
RColorBrewer "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
Rcpp "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
RSQLite "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
Installed Built ReposVer
BiocGenerics "0.18.0" "3.3.0" "0.20.0"
DBI "0.4-1" "3.3.0" "0.5-1"
dichromat "2.0-0" "3.2.3" "2.0-0"
digest "0.6.10" "3.3.2" "0.6.12"
GenomicAlignments "1.8.4" "3.3.1" "1.10.0"
GenomicRanges "1.24.2" "3.3.0" "1.26.3"
gtools "3.5.0" "3.2.3" "3.5.0"
IRanges "2.6.1" "3.3.0" "2.8.1"
labeling "0.3" "3.2.3" "0.3"
locfit "1.5-9.1" "3.2.3" "1.5-9.1"
munsell "0.4.3" "3.2.3" "0.4.3"
R.methodsS3 "1.7.1" "3.2.3" "1.7.1"
R6 "2.1.2" "3.3.0" "2.2.0"
RColorBrewer "1.1-2" "3.2.3" "1.1-2"
Rcpp "0.12.8" "3.3.2" "0.12.9"
RSQLite "1.0.0" "3.2.3" "1.1-2"
Repository
BiocGenerics "https://bioconductor.org/packages/3.4/bioc/src/contrib"
DBI "https://cran.rstudio.com/src/contrib"
dichromat "https://cran.rstudio.com/src/contrib"
digest "https://cran.rstudio.com/src/contrib"
GenomicAlignments "https://bioconductor.org/packages/3.4/bioc/src/contrib"
GenomicRanges "https://bioconductor.org/packages/3.4/bioc/src/contrib"
gtools "https://cran.rstudio.com/src/contrib"
IRanges "https://bioconductor.org/packages/3.4/bioc/src/contrib"
labeling "https://cran.rstudio.com/src/contrib"
locfit "https://cran.rstudio.com/src/contrib"
munsell "https://cran.rstudio.com/src/contrib"
R.methodsS3 "https://cran.rstudio.com/src/contrib"
R6 "https://cran.rstudio.com/src/contrib"
RColorBrewer "https://cran.rstudio.com/src/contrib"
Rcpp "https://cran.rstudio.com/src/contrib"
RSQLite "https://cran.rstudio.com/src/contrib"
[ reached getOption("max.print") -- omitted 2 rows ]
update with biocLite()
* Packages too new for Bioconductor version '3.4'
Version LibPath
nima "0.4.0" "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
tmle.npvi "0.11.2" "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
wesanderson "0.3.4" "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
downgrade with biocLite(c("nima", "tmle.npvi", "wesanderson"))
Error: 18 package(s) out of date; 3 package(s) too new
Thanks for your quick reply, Kasper. I've added the information produced by "traceback()" and "biocValid()" (it seems like the latter of these includes the same information produced by "sessionInfo()").
It looks like the update fixed everything, at least related to the use of `minfi::mapToGenome`. Thanks for your help, Kasper!