Does anyone have any idea how to get Affy 1.0R tiling array data into CHARM? I can't see any mathematical reason why CHARM shouldn't be able to estimate percentage methylation from these files, I just can't get the data structure to set up correctly. I have imported the CEL files in with oligo, and ctrlIdx can identify regions correctly. I just can't get it to estimate percent methylation 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] charm_2.4.0 genefilter_1.40.0 [3] RColorBrewer_1.0-5 fields_6.7 [5] spam_0.29-2 SQN_1.0.5 [7] nor1mix_1.1-3 mclust_4.0 [9] BSgenome.Hsapiens.UCSC.hg18_1.3.19 BSgenome_1.26.1 [11] Biostrings_2.26.2 GenomicRanges_1.10.6 [13] IRanges_1.16.5 pd.hs.prompr.v02_0.0.1 [15] RSQLite_0.11.2 DBI_0.2-5 [17] oligo_1.22.0 Biobase_2.18.0 [19] oligoClasses_1.20.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.2 affyio_1.26.0 annotate_1.36.0 [4] AnnotationDbi_1.20.3 BiocInstaller_1.8.3 bit_1.1-9 [7] codetools_0.2-8 corpcor_1.6.4 ff_2.2-10 [10] foreach_1.4.0 gtools_2.7.0 iterators_1.0.6 [13] limma_3.14.4 MASS_7.3-23 multtest_2.14.0 [16] parallel_2.15.2 preprocessCore_1.20.0 siggenes_1.32.0 [19] splines_2.15.2 stats4_2.15.2 survival_2.37-2 [22] sva_3.4.0 XML_3.95-0.1 xtable_1.7-0 [25] zlibbioc_1.4.0 > -- Sent via the guest posting facility at bioconductor.org.