Hi, I have Illumina 450K data for 570 samples. I have loaded IDAT files into R using minfi. After I ran some QC steps, I'd like to remove sample outliers and probes with large detection P. Is there a straightforward way to do so in minfi? I have searched in Bioconductor mailing list but couldn't find a direct answer. Thank you very much for the help! Donglei Hu, Ph.D. Department of Medicine University of California, San Francisco -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450kmanifest_0.4.0 [2] minfi_1.4.0 [3] Biostrings_2.26.3 [4] GenomicRanges_1.10.7 [5] IRanges_1.16.6 [6] reshape_0.8.4 [7] plyr_1.8 [8] lattice_0.20-15 [9] Biobase_2.18.0 [10] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 annotate_1.36.0 AnnotationDbi_1.20.7 [4] beanplot_1.1 BiocInstaller_1.8.3 bit_1.1-10 [7] codetools_0.2-8 crlmm_1.16.9 DBI_0.2-7 [10] ellipse_0.3-8 ff_2.2-11 foreach_1.4.1 [13] genefilter_1.40.0 grid_2.15.3 iterators_1.0.6 [16] limma_3.14.4 MASS_7.3-23 Matrix_1.0-12 [19] matrixStats_0.8.1 mclust_4.1 multtest_2.14.0 [22] mvtnorm_0.9-9995 nor1mix_1.1-4 oligoClasses_1.20.0 [25] parallel_2.15.3 preprocessCore_1.20.0 RColorBrewer_1.0-5 [28] RcppEigen_0.3.1.2.1 R.methodsS3_1.4.4 RSQLite_0.11.4 [31] siggenes_1.32.0 splines_2.15.3 stats4_2.15.3 [34] survival_2.37-4 XML_3.98-1.1 xtable_1.7-1 [37] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Donglei Hu, On 7/24/2013 2:52 PM, Donglei Hu [guest] wrote: > Hi, > > I have Illumina 450K data for 570 samples. I have loaded IDAT files into R using minfi. After I ran some QC steps, I'd like to remove sample outliers and probes with large detection P. Is there a straightforward way to do so in minfi? I have searched in Bioconductor mailing list but couldn't find a direct answer. Thank you very much for the help! All the objects in minfi are extensions of either ExpressionSet or SummarizedExperiment, which are both intended to 'do the right thing' under row selection. So all you need to do is myminfi.object.filtered <- myoriginalminfiobject[rowsToKeep,] And I would recommend upgrading R to 3.0.1. minfi in particular has seen quite a bit of development. Best, Jim > > Donglei Hu, Ph.D. > Department of Medicine > University of California, San Francisco > > -- output of sessionInfo(): > > R version 2.15.3 (2013-03-01) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IlluminaHumanMethylation450kmanifest_0.4.0 > [2] minfi_1.4.0 > [3] Biostrings_2.26.3 > [4] GenomicRanges_1.10.7 > [5] IRanges_1.16.6 > [6] reshape_0.8.4 > [7] plyr_1.8 > [8] lattice_0.20-15 > [9] Biobase_2.18.0 > [10] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 annotate_1.36.0 AnnotationDbi_1.20.7 > [4] beanplot_1.1 BiocInstaller_1.8.3 bit_1.1-10 > [7] codetools_0.2-8 crlmm_1.16.9 DBI_0.2-7 > [10] ellipse_0.3-8 ff_2.2-11 foreach_1.4.1 > [13] genefilter_1.40.0 grid_2.15.3 iterators_1.0.6 > [16] limma_3.14.4 MASS_7.3-23 Matrix_1.0-12 > [19] matrixStats_0.8.1 mclust_4.1 multtest_2.14.0 > [22] mvtnorm_0.9-9995 nor1mix_1.1-4 oligoClasses_1.20.0 > [25] parallel_2.15.3 preprocessCore_1.20.0 RColorBrewer_1.0-5 > [28] RcppEigen_0.3.1.2.1 R.methodsS3_1.4.4 RSQLite_0.11.4 > [31] siggenes_1.32.0 splines_2.15.3 stats4_2.15.3 > [34] survival_2.37-4 XML_3.98-1.1 xtable_1.7-1 > [37] zlibbioc_1.4.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099