Using getControlTypes() gives an error

[lckarssen]

I tried to get a list of the control probe types of the example manifest using getControlTypes(), but I get the following output:

> getControlTypes(IlluminaHumanMethylation450kmanifest)
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript contains invalid names

This was after loading the minfi and minfiData packages. Using the following works fine:

> unique(getProbeInfo(IlluminaHumanMethylation450kmanifest, type="Control")$Type)
 [1] "STAINING"                "EXTENSION"
 [3] "HYBRIDIZATION"           "TARGET REMOVAL"
 [5] "BISULFITE CONVERSION I"  "BISULFITE CONVERSION II"
 [7] "SPECIFICITY I"           "SPECIFICITY II"
 [9] "NON-POLYMORPHIC"         "NEGATIVE"
[11] "RESTORATION"             "NORM_A"
[13] "NORM_G"                  "NORM_C"
[15] "NORM_T"

My sessionInfo():

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] minfiData_0.12.0
 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [3] IlluminaHumanMethylation450kmanifest_0.4.0
 [4] minfi_1.16.0
 [5] bumphunter_1.10.0
 [6] locfit_1.5-9.1
 [7] iterators_1.0.8
 [8] foreach_1.4.3
 [9] Biostrings_2.38.2
[10] XVector_0.10.0
[11] SummarizedExperiment_1.0.1
[12] GenomicRanges_1.22.2
[13] GenomeInfoDb_1.6.1
[14] IRanges_2.4.6
[15] S4Vectors_0.8.5
[16] lattice_0.20-33
[17] Biobase_2.30.0
[18] BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] mclust_5.1              rgl_0.95.1247           base64_1.1
 [4] Rcpp_0.12.2             corpcor_1.6.8           Rsamtools_1.22.0
 [7] digest_0.6.8            plyr_1.8.3              futile.options_1.0.0
[10] ellipse_0.3-8           RSQLite_1.0.0           ggplot2_2.0.0
[13] zlibbioc_1.16.0         GenomicFeatures_1.22.7  annotate_1.48.0
[16] preprocessCore_1.32.0   splines_3.2.3           BiocParallel_1.4.3
[19] stringr_1.0.0           igraph_1.0.1            RCurl_1.95-4.7
[22] biomaRt_2.26.1          munsell_0.4.2           rtracklayer_1.30.1
[25] multtest_2.26.0         pkgmaker_0.22           GEOquery_2.36.0
[28] quadprog_1.5-5          codetools_0.2-14        matrixStats_0.50.1
[31] XML_3.98-1.3            reshape_0.8.5           GenomicAlignments_1.6.1
[34] MASS_7.3-45             bitops_1.0-6            grid_3.2.3
[37] nlme_3.1-122            xtable_1.8-0            gtable_0.1.2
[40] registry_0.3            DBI_0.3.1               magrittr_1.5
[43] scales_0.3.0            stringi_1.0-1           genefilter_1.52.0
[46] doRNG_1.6               limma_3.26.3            futile.logger_1.4.1
[49] nor1mix_1.2-1           lambda.r_1.1.7          RColorBrewer_1.1-2
[52] mixOmics_5.2.0          siggenes_1.44.0         tools_3.2.3
[55] illuminaio_0.12.0       rngtools_1.2.4          survival_2.38-3
[58] colorspace_1.2-6        AnnotationDbi_1.32.2    beanplot_1.2

[kasperdanielhansen]

Hmm, this is unexpected. I'll have a look but it'll be a while due to the holidays.

Best, Kasper (Sent from my phone.)

On Dec 23, 2015, at 07:22, L.C. Karssen notifications@github.com wrote:

I tried to get a list of the control probe types of the example manifest using getControlTypes(), but I get the following output:

getControlTypes(IlluminaHumanMethylation450kmanifest) Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allowappend) : subscript contains invalid names This was after loading the minfi and minfiData packages Using the following works fine:

unique(getProbeInfo(IlluminaHumanMethylation450kmanifest, type="Control")$Type) [1] "STAINING" "EXTENSION" [3] "HYBRIDIZATION" "TARGET REMOVAL" [5] "BISULFITE CONVERSION I" "BISULFITE CONVERSION II" [7] "SPECIFICITY I" "SPECIFICITY II" [9] "NON-POLYMORPHIC" "NEGATIVE" [11] "RESTORATION" "NORM_A" [13] "NORM_G" "NORM_C" [15] "NORM_T" My sessionInfo():

sessionInfo() R version 323 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 1510

locale: [1] LC_CTYPE=en_USUTF-8 LC_NUMERIC=C [3] LC_TIME=nl_NLUTF-8 LC_COLLATE=en_USUTF-8 [5] LC_MONETARY=nl_NLUTF-8 LC_MESSAGES=en_USUTF-8 [7] LC_PAPER=nl_NLUTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=nl_NLUTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] minfiData_0120 [2] IlluminaHumanMethylation450kannoilmn12hg19_021 [3] IlluminaHumanMethylation450kmanifest_040 [4] minfi_1160 [5] bumphunter_1100 [6] locfit_15-91 [7] iterators_108 [8] foreach_143 [9] Biostrings_2382 [10] XVector_0100 [11] SummarizedExperiment_101 [12] GenomicRanges_1222 [13] GenomeInfoDb_161 [14] IRanges_246 [15] S4Vectors_085 [16] lattice_020-33 [17] Biobase_2300 [18] BiocGenerics_0161

loaded via a namespace (and not attached): [1] mclust_51 rgl_0951247 base64_11 [4] Rcpp_0122 corpcor_168 Rsamtools_1220 [7] digest_068 plyr_183 futileoptions_100 [10] ellipse_03-8 RSQLite_100 ggplot2_200 [13] zlibbioc_1160 GenomicFeatures_1227 annotate_1480 [16] preprocessCore_1320 splines_323 BiocParallel_143 [19] stringr_100 igraph_101 RCurl_195-47 [22] biomaRt_2261 munsell_042 rtracklayer_1301 [25] multtest_2260 pkgmaker_022 GEOquery_2360 [28] quadprog_15-5 codetools_02-14 matrixStats_0501 [31] XML_398-13 reshape_085 GenomicAlignments_161 [34] MASS_73-45 bitops_10-6 grid_323 [37] nlme_31-122 xtable_18-0 gtable_012 [40] registry_03 DBI_031 magrittr_15 [43] scales_030 stringi_10-1 genefilter_1520 [46] doRNG_16 limma_3263 futilelogger_141 [49] nor1mix_12-1 lambdar_117 RColorBrewer_11-2 [52] mixOmics_520 siggenes_1440 tools_323 [55] illuminaio_0120 rngtools_124 survival_238-3 [58] colorspace_12-6 AnnotationDbi_1322 beanplot_12 — Reply to this email directly or view it on GitHub.

[lckarssen]

Thanks for the quick reply. No problem w.r.t. the holidays. The unique(getProbeInfo(...)) line gives me what I want.

Maybe of note: I upgraded to minfi 1.16.0 today. Before I was running 1.10.2 (minfiData v0.6.0), where I got the following error:

> getControlTypes(IlluminaHumanMethylation450kmanifest)
Error in normalizeSingleBracketSubscript(j, x) : 
  subscript contains invalid names

[kasperdanielhansen]

I forgot about this, but have returned to it. Basically, this function has always thrown an error, so I have removed it. Use getProbeInfo(type = "Control") instead

[lckarssen]

To be honest, I forgot about it too :-). Using getProbeInfo was indeed the solution I went for. Thanks.