IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?
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Ed Schwalbe ▴ 10
@ed-schwalbe-6024
Last seen 8.0 years ago
United Kingdom
> James W. MacDonald <jmacdon at="" ...=""> writes: > You would be better off using the FDb.InfiniumMethylation.hg19 package, > which not only has all the locations for the probes, but also has them > in a more useful format. > > > library(FDb.InfiniumMethylation.hg19) > > x <- get450k() > Warning message: > In if is.na(genome(GR))) { : > the condition has length > 1 and only the first element will be used > > x > GRanges with 485577 ranges and 7 metadata columns: > seqnames ranges strand | addressA addressB > channel > <rle> <iranges> <rle> | <rle> <rle> <rle> > cg13869341 chr1 [15865, 15866] * | 62703328 > 16661461 Red > cg14008030 chr1 [18827, 18828] * | 27651330 <na> Both > cg12045430 chr1 [29407, 29408] * | 25703424 > 34666387 Red > cg20826792 chr1 [29425, 29426] * | 61731400 > 14693326 Red > cg00381604 chr1 [29435, 29436] * | 26752380 > 50693408 Red Does anyone know why Jim's lines of code do not work on my R installation (R3.0.1)? Many thanks, Ed library(FDb.InfiniumMethylation.hg19) x <- get450k() Error in `seqinfo<-`(`*tmp*`, value = NULL) : the supplied 'seqinfo' must be a Seqinfo object In addition: Warning message: In if is.na(genome(GR))) { : the condition has length > 1 and only the first element will be used sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C [6] LC_MESSAGES=C LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_2.0.7 org.Hs.eg.db_2.9.0 [3] RSQLite_0.11.4 DBI_0.2-7 [5] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2 [7] GenomicFeatures_1.12.2 AnnotationDbi_1.22.6 [9] BiocInstaller_1.10.2 minfi_1.6.0 [11] Biostrings_2.28.0 GenomicRanges_1.12.4 [13] IRanges_1.18.1 reshape_0.8.4 [15] plyr_1.8 lattice_0.20-15 [17] Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] BSgenome_1.28.0 MASS_7.3-26 R.methodsS3_1.4.4 RColorBrewer_1.0-5 RCurl_1.95-4.1 [6] Rsamtools_1.12.3 XML_3.98-1.1 beanplot_1.1 biomaRt_2.16.0 bitops_1.0-5 [11] grid_3.0.1 illuminaio_0.2.0 limma_3.16.5 matrixStats_0.8.1 mclust_4.1 [16] multtest_2.16.0 nor1mix_1.1-4 preprocessCore_1.22.0 siggenes_1.34.0 splines_3.0.1 [21] stats4_3.0.1 survival_2.37-4 tools_3.0.1 zlibbioc_1.6.0
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Simone ▴ 180
@simone-5854
Last seen 4.7 years ago
> Does anyone know why Jim's lines of code do not work on my R installation > (R3.0.1)? > > library(FDb.InfiniumMethylation.hg19) > x <- get450k() > Error in `seqinfo<-`(`*tmp*`, value = NULL) : > the supplied 'seqinfo' must be a Seqinfo object > In addition: Warning message: > In if is.na(genome(GR))) { : > the condition has length > 1 and only the first element will be used Yes, I get exactly the same error with R version 3.0.1 (2013-05-16) on x86_64-pc-linux-gnu 64-bit (see sessionInfo() of my initial posting)! Simone
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VSM ▴ 120
@vsm-6019
Last seen 4.8 years ago
United Kingdom
Hi Simone, I think the answer to your seqinfo error when using get450k() is found here: https://mailman.stat.ethz.ch/pipermail/bioconductor/2012-October/04876 6.html Installing BSgenome.Hsapiens.UCSC.hg19 fixed it for me too. Victoria -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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