Dear members, I have methylation data for 4 tumor and 5 normal cases from Illumina 450k array in iDAT format. I used methylumi package to read the idat files in R. I am unable to get a way to export the probes with the intensity values and corresponding genomic position (say TSS200, TSS1500 etc.). I want to see the differences in methylation at different sites across tumor normal. Please help. I use the following commands: > barcodes<-c("8963303122_R01C01","8963303122_R01C02","8963303122_R02C02 ","8963303122_R04C01","8963303122_R04C02","8963303122_R05C01","8963303 122_R06C01","8963303142_R01C01","8963303142_R02C01","8963303142_R03C01 ") > lumiset<-methylumIDAT(barcodes) > normalized<-normalizeMethyLumiSet(lumiset) > write.table(file="normalized_beta_values.tsv",quote=F,sep="\t",data.fr ame(betas(normalized))) sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_1.4.7 org.Hs.eg.db_2.8.0 [3] RSQLite_0.11.2 DBI_0.2-5 [5] AnnotationDbi_1.20.3 methylumi_2.4.0 [7] ggplot2_0.9.3 reshape2_1.2.2 [9] scales_0.2.3 Biobase_2.18.0 [11] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] annotate_1.36.0 colorspace_1.2-1 dichromat_2.0-0 digest_0.6.3 [5] genefilter_1.40.0 grid_2.15.0 gtable_0.1.2 IRanges_1.16.6 [9] labeling_0.1 lattice_0.20-10 MASS_7.3-23 munsell_0.4 [13] parallel_2.15.0 plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 [17] splines_2.15.0 stats4_2.15.0 stringr_0.6.2 survival_2.37-2 [21] tools_2.15.0 XML_3.95-0.1 xtable_1.7-1 Thanks in advance, Srikanth -- Srinivas Srikanth Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+919019114878, India [[alternative HTML version deleted]]

Dear members, I have methylation data for 4 tumor and 5 normal cases from Illumina 450k array in iDAT format. I used methylumi package to read the idat files in R. I am unable to get a way to export the probes with the intensity values and corresponding genomic position (say TSS200, TSS1500 etc.). I want to see the differences in methylation at different sites across tumor normal. Please help. I use the following commands: > barcodes<-c("8963303122_R01C01","8963303122_R01C02","8963303122_R02C02 ","8963303122_R04C01","8963303122_R04C02","8963303122_R05C01","8963303 122_R06C01","8963303142_R01C01","8963303142_R02C01","8963303142_R03C01 ") > lumiset<-methylumIDAT(barcodes) > normalized<-normalizeMethyLumiSet(lumiset) > write.table(file="normalized_beta_values.tsv",quote=F,sep="\t",data.fr ame(betas(normalized))) sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_1.4.7 org.Hs.eg.db_2.8.0 [3] RSQLite_0.11.2 DBI_0.2-5 [5] AnnotationDbi_1.20.3 methylumi_2.4.0 [7] ggplot2_0.9.3 reshape2_1.2.2 [9] scales_0.2.3 Biobase_2.18.0 [11] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] annotate_1.36.0 colorspace_1.2-1 dichromat_2.0-0 digest_0.6.3 [5] genefilter_1.40.0 grid_2.15.0 gtable_0.1.2 IRanges_1.16.6 [9] labeling_0.1 lattice_0.20-10 MASS_7.3-23 munsell_0.4 [13] parallel_2.15.0 plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 [17] splines_2.15.0 stats4_2.15.0 stringr_0.6.2 survival_2.37-2 [21] tools_2.15.0 XML_3.95-0.1 xtable_1.7-1 Thanks in advance, Srikanth -- Srinivas Srikanth Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+919019114878, India [[alternative HTML version deleted]]