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Question: Large datasets in methylumi
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4.9 years ago by
Guest User12k
Guest User12k wrote:
Hi, I am trying to analyse a large dataset in methylumi - 300 samples on HumanMethylation450 arrays. I get the following error message if I try and analyse the dataset whole: lumi450 <- methylumIDAT(meth450barcodes,idatPath=getwd(),parallel=TRUE) Error in annotation(NChannelSet) : error in evaluating the argument 'object' in selecting a method for function 'annotation': Error in x[[assay]] : subscript out of bounds If I split the dataset into three it works fine, but I'd rather run the analysis whole for simplicity. I have 32gb of system RAM and looking at top it doesn't look like R is running out of memory. Any suggestions? -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] methylumi_2.4.0 ggplot2_0.9.3 reshape2_1.2.2 scales_0.2.3 [5] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationDbi_1.20.3 colorspace_1.2-0 [4] DBI_0.2-5 dichromat_1.2-4 digest_0.6.0 [7] grid_2.15.2 gtable_0.1.2 IRanges_1.16.4 [10] labeling_0.1 lattice_0.20-10 MASS_7.3-22 [13] munsell_0.4 plyr_1.8 proto_0.3-9.2 [16] RColorBrewer_1.0-5 RSQLite_0.11.2 stats4_2.15.2 [19] stringr_0.6.2 tools_2.15.2 XML_3.95-0.1 [22] xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.
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