import only partial samples of an array
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Guest User ★ 12k
@guest-user-4897
Last seen 8.1 years ago
Hi, I was wondering whether it was possible to only import the first few samples of an array using the lumiR or lumiR.batch function. -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.12.0 Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 AnnotationDbi_1.22.6 beanplot_1.1 BiocInstaller_1.10.3 Biostrings_2.28.0 colorspace_1.2-2 [9] DBI_0.2-7 GenomicRanges_1.12.5 grid_3.0.1 illuminaio_0.2.0 IRanges_1.18.3 KernSmooth_2.23-10 lattice_0.20-15 limma_3.16.7 [17] MASS_7.3-26 Matrix_1.0-12 matrixStats_0.8.5 mclust_4.2 methylumi_2.6.1 mgcv_1.7-22 minfi_1.6.0 multtest_2.16.0 [25] nleqslv_2.0 nlme_3.1-109 nor1mix_1.1-4 preprocessCore_1.22.0 R.methodsS3_1.4.4 RColorBrewer_1.0-5 reshape_0.8.4 RSQLite_0.11.4 [33] siggenes_1.34.0 splines_3.0.1 stats4_3.0.1 survival_2.37-4 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
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Pan Du ▴ 440
@pan-du-4636
Last seen 8.1 years ago
Hi Chris There is another function: lumiR.batch for you purpose. You can define the samples you want to input in the "sampleInfoFile" parameter. Check the help of "lumiR.batch" for more details. Pan On Wed, Aug 28, 2013 at 6:47 AM, Chris [guest] <guest@bioconductor.org>wrote: > > Hi, I was wondering whether it was possible to only import the first few > samples of an array using the lumiR or lumiR.batch function. > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] lumi_2.12.0 Biobase_2.20.1 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 > AnnotationDbi_1.22.6 beanplot_1.1 BiocInstaller_1.10.3 > Biostrings_2.28.0 colorspace_1.2-2 > [9] DBI_0.2-7 GenomicRanges_1.12.5 grid_3.0.1 > illuminaio_0.2.0 IRanges_1.18.3 KernSmooth_2.23-10 > lattice_0.20-15 limma_3.16.7 > [17] MASS_7.3-26 Matrix_1.0-12 matrixStats_0.8.5 > mclust_4.2 methylumi_2.6.1 mgcv_1.7-22 > minfi_1.6.0 multtest_2.16.0 > [25] nleqslv_2.0 nlme_3.1-109 nor1mix_1.1-4 > preprocessCore_1.22.0 R.methodsS3_1.4.4 RColorBrewer_1.0-5 > reshape_0.8.4 RSQLite_0.11.4 > [33] siggenes_1.34.0 splines_3.0.1 stats4_3.0.1 > survival_2.37-4 XML_3.95-0.2 xtable_1.7-1 > zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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