library("methylumi") barcodes <- paste(5900438005, paste(paste("R0", rep(1:6, 2), sep=""), paste("C0", rep(1:2, each=6), sep=""), sep=""), sep="_") lumi450k <- methylumIDAT(barcodes, idatPath="5900438005/") normLumi450k <- normalizeMethyLumiSet(lumi450k) So far so good; I can extract betas, etc. But the qcplots won't work: qcplot(normLumi450k, controlTypes(normLumi450k)[1]) Error in as.table.default(x) : cannot coerce into a table Thanks for any pointers, -Aaron > sessionInfo() R Under development (unstable) (2011-11-06 r57590) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] minfi_1.1.2 lattice_0.20-0 ggplot2_0.8.9 proto_0.3-9.2 [5] reshape_0.8.4 plyr_1.7.1 matrixStats_0.4.3 R.methodsS3_1.2.1 [9] methylumi_2.1.13 IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.6.4 RSQLite_0.11.1 [13] DBI_0.2-5 AnnotationDbi_1.17.21 Biobase_2.15.3 BiocGenerics_0.1.4 [17] BiocInstaller_1.3.7 loaded via a namespace (and not attached): [1] Biostrings_2.23.6 IRanges_1.13.24 MASS_7.3-17 RColorBrewer_1.0-5 affyio_1.23.1 annotate_1.33.2 beanplot_1.1 [8] bit_1.1-8 crlmm_1.13.9 ellipse_0.3-5 ff_2.2-5 genefilter_1.37.0 limma_3.11.11 mclust_3.4.11 [15] multtest_2.11.2 mvtnorm_0.9-9992 nor1mix_1.1-3 oligoClasses_1.17.24 preprocessCore_1.17.1 siggenes_1.29.5 splines_2.15.0 [22] survival_2.36-12 tools_2.15.0 xtable_1.7-0 zlibbioc_1.1.1 [[alternative HTML version deleted]]

try qc.probe.plot() On Fri, Feb 17, 2012 at 10:46 AM, Aaron Mackey <amackey@virginia.edu> wrote: > library("methylumi") > barcodes <- paste(5900438005, > paste(paste("R0", rep(1:6, 2), sep=""), > paste("C0", rep(1:2, each=6), sep=""), > sep=""), > sep="_") > > lumi450k <- methylumIDAT(barcodes, > idatPath="5900438005/") > normLumi450k <- normalizeMethyLumiSet(lumi450k) > > So far so good; I can extract betas, etc. But the qcplots won't work: > > qcplot(normLumi450k, controlTypes(normLumi450k)[1]) > > Error in as.table.default(x) : cannot coerce into a table > > Thanks for any pointers, > > -Aaron > > > sessionInfo() > R Under development (unstable) (2011-11-06 r57590) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] minfi_1.1.2 lattice_0.20-0 > ggplot2_0.8.9 proto_0.3-9.2 > > [5] reshape_0.8.4 plyr_1.7.1 > matrixStats_0.4.3 R.methodsS3_1.2.1 > > [9] methylumi_2.1.13 > IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.6.4 > RSQLite_0.11.1 > [13] DBI_0.2-5 AnnotationDbi_1.17.21 > Biobase_2.15.3 BiocGenerics_0.1.4 > > [17] BiocInstaller_1.3.7 > > loaded via a namespace (and not attached): > [1] Biostrings_2.23.6 IRanges_1.13.24 MASS_7.3-17 > RColorBrewer_1.0-5 affyio_1.23.1 annotate_1.33.2 > beanplot_1.1 > [8] bit_1.1-8 crlmm_1.13.9 ellipse_0.3-5 > ff_2.2-5 genefilter_1.37.0 limma_3.11.11 > mclust_3.4.11 > [15] multtest_2.11.2 mvtnorm_0.9-9992 nor1mix_1.1-3 > oligoClasses_1.17.24 preprocessCore_1.17.1 siggenes_1.29.5 > splines_2.15.0 > [22] survival_2.36-12 tools_2.15.0 xtable_1.7-0 > zlibbioc_1.1.1 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]