Question: minfi "mapToGenome" dimension error
0
gravatar for nhejazi
2.4 years ago by
nhejazi0
UC Berkeley
nhejazi0 wrote:

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by nhejazi0
Answer: minfi "mapToGenome" dimension error
0
gravatar for Kasper Daniel Hansen
2.4 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
Could you run your code and then immediately when you get an error do traceback() Also give us output of sessionInfo() biocValid() The last might require that you source biocLite Best, Kasper (Sent from my phone.) > On Mar 8, 2017, at 03:17, nhejazi [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User nhejazi wrote Question: minfi "mapToGenome" dimension error: > > 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. > > Post tags: methylation, epic microarray, minfi, methylationepic > > You may reply via email or visit minfi "mapToGenome" dimension error
ADD COMMENTlink written 2.4 years ago by Kasper Daniel Hansen6.4k

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()").

ADD REPLYlink written 2.4 years ago by nhejazi0
You have multiple packages which are out of date and which minfi depends on. Update and try again. The output of biocValid() should preferably be TRUE. What is the output of ncol(ratioset_raw)? 1? On Wed, Mar 8, 2017 at 1:58 PM, nhejazi [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User nhejazi <https: support.bioconductor.org="" u="" 10825=""/> wrote Comment: > minfi "mapToGenome" dimension error > <https: support.bioconductor.org="" p="" 93518="" #93585="">: > > 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()"). > > ------------------------------ > > Post tags: methylation, epic microarray, minfi, methylationepic > > You may reply via email or visit https://support.bioconductor. > org/p/93518/#93585 >
ADD REPLYlink written 2.4 years ago by Kasper Daniel Hansen6.4k

It looks like the update fixed everything, at least related to the use of `minfi::mapToGenome`. Thanks for your help, Kasper!

ADD REPLYlink written 2.4 years ago by nhejazi0
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