Hi Does anyone have any pointers about coercing Agilent two colour methylation array data into CHARM? Specifically I would like to import some raw data files from GEO into CHARM for analysis. These files are from a variety of Agilent methylation microarrays. BW Andrew -- 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] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0 [3] oligoClasses_1.20.0 RSQLite_0.11.2 [5] DBI_0.2-5 charm_2.4.0 [7] genefilter_1.40.0 RColorBrewer_1.0-5 [9] fields_6.7 spam_0.29-2 [11] SQN_1.0.5 nor1mix_1.1-3 [13] mclust_4.0 Biobase_2.18.0 [15] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affyio_1.26.0 annotate_1.36.0 [4] AnnotationDbi_1.20.3 BiocInstaller_1.8.3 Biostrings_2.26.2 [7] bit_1.1-9 BSgenome_1.26.1 codetools_0.2-8 [10] corpcor_1.6.4 ff_2.2-10 foreach_1.4.0 [13] GenomicRanges_1.10.5 gtools_2.7.0 IRanges_1.16.4 [16] iterators_1.0.6 limma_3.14.3 MASS_7.3-22 [19] multtest_2.14.0 parallel_2.15.2 preprocessCore_1.20.0 [22] siggenes_1.32.0 splines_2.15.2 stats4_2.15.2 [25] survival_2.37-2 sva_3.4.0 tools_2.15.2 [28] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.