Entering edit mode
Hi Everyone,
Im currently trying to analyse a large number of EPIC arrays and I'm getting an odd package error that seems to come about when I add annotation to the array object
rgSet <- read.metharray.exp(targets = targets)
getManifest(rgSet)
annotation(rgSet)[1] <- "IlluminaHumanMethylationEPIC" annotation(rgSet)[2] <- "ilm10b2.hg19"
mSet <- preprocessSWAN(rgSet)
detP <- detectionP(rgSet) keep <- rowSums(detP < 0.05) == ncol(rgSet) mSet <- mSet[keep,]
dim(mSet)
RSet <- ratioConvert(mSet, what = "both", keepCN = TRUE) GRset <- mapToGenome(RSet)
It completes fine, but when looking at RSet or GRset I get:
RSet <- ratioConvert(mSet, what = "both", keepCN = TRUE)
> RSet
class: RatioSet
dim: 848005 192
metadata(0):
assays(3): Beta M CN
rownames(848005): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(192): 201236470086_R01C01 201236470086_R02C01 ... 201364910019_R05C01
201364910105_R05C01
colData names(9): Sample_Name Sample_Well ... Basename filenames
Annotation
Error in seq.default(along = annotation) :
(converted from warning) partial argument match of 'along' to 'along.with'
I know this is just probably a package conflict and that it does look like seq.default has changed an argument from along to along.with, but considering the basic nature of this function in an array analysis pipeline, I was wondering whether anyone had seen this before?
Cheers
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8
[4] LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] pander_0.6.0
[2] stringr_1.2.0
[3] Rgraphviz_2.20.0
[4] GMCM_1.2.4
[5] GOstats_2.42.0
[6] graph_1.54.0
[7] Category_2.42.1
[8] Matrix_1.2-10
[9] GO.db_3.4.1
[10] biomaRt_2.32.1
[11] RColorBrewer_1.1-2
[12] gridExtra_2.2.1
[13] qqman_0.1.4
[14] pheatmap_1.0.8
[15] methylumi_2.22.0
[16] FDb.InfiniumMethylation.hg19_2.2.0
[17] org.Hs.eg.db_3.4.1
[18] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[19] GenomicFeatures_1.28.4
[20] AnnotationDbi_1.38.2
[21] reshape2_1.4.2
[22] scales_0.4.1
[23] limma_3.32.5
[24] ggbio_1.24.1
[25] ggrepel_0.6.5
[26] magrittr_1.5
[27] plyr_1.8.4
[28] readxl_1.0.0
[29] dplyr_0.7.2
[30] purrr_0.2.3
[31] readr_1.1.1
[32] tidyr_0.6.3
[33] tibble_1.3.3
[34] ggplot2_2.2.1
[35] tidyverse_1.1.1
[36] missMethyl_1.10.0
[37] IlluminaHumanMethylationEPICmanifest_0.3.0
[38] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[39] BiocInstaller_1.26.0
[40] minfi_1.22.1
[41] bumphunter_1.16.0
[42] locfit_1.5-9.1
[43] iterators_1.0.8
[44] foreach_1.4.3
[45] Biostrings_2.44.2
[46] XVector_0.16.0
[47] SummarizedExperiment_1.6.3
[48] DelayedArray_0.2.7
[49] matrixStats_0.52.2
[50] Biobase_2.36.2
[51] GenomicRanges_1.28.4
[52] GenomeInfoDb_1.12.2
[53] IRanges_2.10.2
[54] S4Vectors_0.14.3
[55] BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] RSQLite_2.0
[2] htmlwidgets_0.9
[3] BiocParallel_1.10.1
[4] munsell_0.4.3
[5] codetools_0.2-15
[6] preprocessCore_1.38.1
[7] statmod_1.4.30
[8] colorspace_1.3-2
[9] OrganismDbi_1.18.0
[10] knitr_1.16
[11] GenomeInfoDbData_0.99.0
[12] mnormt_1.5-5
[13] bit64_0.9-7
[14] biovizBase_1.24.0
[15] R6_2.2.2
[16] illuminaio_0.18.0
[17] AnnotationFilter_1.0.0
[18] bitops_1.0-6
[19] reshape_0.8.6
[20] assertthat_0.2.0
[21] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[22] nnet_7.3-12
[23] gtable_0.2.0
[24] ensembldb_2.0.3
[25] rlang_0.1.1
[26] genefilter_1.58.1
[27] calibrate_1.7.2
[28] splines_3.4.0
[29] rtracklayer_1.36.4
[30] lazyeval_0.2.0
[31] acepack_1.4.1
[32] GEOquery_2.42.0
[33] dichromat_2.0-0
[34] broom_0.4.2
[35] checkmate_1.8.3
[36] yaml_2.1.14
[37] modelr_0.1.1
[38] backports_1.1.0
[39] httpuv_1.3.5
[40] Hmisc_4.0-3
[41] RBGL_1.52.0
[42] tools_3.4.0
[43] psych_1.7.5
[44] nor1mix_1.2-2
[45] siggenes_1.50.0
[46] Rcpp_0.12.12
[47] base64enc_0.1-3
[48] zlibbioc_1.22.0
[49] RCurl_1.95-4.8
[50] BiasedUrn_1.07
[51] rpart_4.1-11
[52] openssl_0.9.6
[53] haven_1.1.0
[54] cluster_2.0.6
[55] data.table_1.10.4
[56] ProtGenerics_1.8.0
[57] hms_0.3
[58] mime_0.5
[59] xtable_1.8-2
[60] XML_3.98-1.9
[61] mclust_5.3
[62] compiler_3.4.0
[63] htmltools_0.3.6
[64] Formula_1.2-2
[65] lubridate_1.6.0
[66] DBI_0.7
[67] MASS_7.3-47
[68] quadprog_1.5-5
[69] bindr_0.1
[70] forcats_0.2.0
[71] pkgconfig_2.0.1
[72] GenomicAlignments_1.12.1
[73] registry_0.3
[74] IlluminaHumanMethylation450kmanifest_0.4.0
[75] foreign_0.8-69
[76] xml2_1.1.1
[77] annotate_1.54.0
[78] rngtools_1.2.4
[79] pkgmaker_0.22
[80] multtest_2.32.0
[81] beanplot_1.2
[82] ruv_0.9.6
[83] AnnotationForge_1.18.1
[84] rvest_0.3.2
[85] doRNG_1.6.6
[86] VariantAnnotation_1.22.3
[87] digest_0.6.12
[88] base64_2.0
[89] cellranger_1.1.0
[90] htmlTable_1.9
[91] GSEABase_1.38.0
[92] curl_2.8.1
[93] shiny_1.0.3
[94] Rsamtools_1.28.0
[95] nlme_3.1-131
[96] jsonlite_1.5
[97] bindrcpp_0.2
[98] BSgenome_1.44.0
[99] lattice_0.20-35
[100] GGally_1.3.2
[ reached getOption("max.print") -- omitted 10 entries ]
>
In addition, it appears your code won't even work as written:
> rawdat class: RGChannelSet dim: 1051943 32 metadata(0): assays(2): Green Red rownames(1051943): 1600101 1600111 ... 99810990 99810992 rowData names(0): colnames(32): 201172580002_R01C01 201172580002_R02C01 ... 201172580056_R07C01 201172580056_R08C01 colData names(9): Sample_Name Sample_Well ... Basename filenames Annotation array: IlluminaHumanMethylationEPIC annotation: ilm10b2.hg19 > notok <- rawdat > annotation(notok) <- c("IlluminaHumanMethylationEPIC","ilm10b2.hg19") > notok class: RGChannelSet dim: 1051943 32 metadata(0): assays(2): Green Red rownames(1051943): 1600101 1600111 ... 99810990 99810992 rowData names(0): colnames(32): 201172580002_R01C01 201172580002_R02C01 ... 201172580056_R07C01 201172580056_R08C01 colData names(9): Sample_Name Sample_Well ... Basename filenames Annotation > notok <- preprocessSWAN(notok) Error in .getManifestString(object@annotation) : unable to get the manifest string for this object > getManifest(notok) Error in .getManifestString(object@annotation) : unable to get the manifest string for this objectI was following the advice of someone on the support site which called to manually add EPIC annotations to overwrite the 450K annotation.
Agreed. Even without doing that I'm getting an error:
This line:
Says, in essence, that you would have got a warning because
seq.defaultused partial matching to match the argument 'along' to its actual argument of 'along.which'. But this was converted from a warning to an error because you have the 'warn' option set to 2 or larger, and are converting simple warnings into errors. From ?options'warn': sets the handling of warning messages. If 'warn' is negative all warnings are ignored. If 'warn' is zero (the default) warnings are stored until the top-level function returns. If 10 or fewer warnings were signalled they will be printed otherwise a message saying how many were signalled. An object called 'last.warning' is created and can be printed through the function 'warnings'. If 'warn' is one, warnings are printed as they occur. If 'warn' is two or larger all warnings are turned into errors.There are very few reasons to have warnings converted to errors, and I would not recommend that setting for general use.
Great. Thanks for that explanation