Dear all, started playing with lumi and samples from Illumina 450k arrays; slowly learning how to process the data. One task I still need to figure out is how to get lumi to accept the control probe information exported from BeadStudio. Does someone have pointers to the expected data format, or a working script and toy data they wouldn't mind sharing so I can check for differences between my exported files and those that work? Minimal examples are a bit difficult due to the required files, but maybe I can summarize: 1. Importing exported sample methylation data with lumiMethyR works fine 2. Trying to use the 'controlData' argument fails for the provided control probe file as the import expects a [SAMPLE METHYLATION PROFILE] block which isn't present in the control data: > lumiData <- lumiMethyR(sampleMeth, lib=annot, controlData=sampleControl) Error in .getFinalReportBlock(filename, blockname = blockname, blocks = blocks, : The block called "[SAMPLE METHYLATION PROFILE]" in the file "/data/A_Control_Probe_Profile.txt" is not present and needs to be. Please re-export from bead studio. A quick check confirms that the Sample methylation profile block is only present in the sample file, not the control file (as expected): -- > head -n 10 A_Control_Probe_Profile.tx [Header] GSGX Version 1.1.0 Report Date 11/18/2011 5:08:30 PM Project A Group Set A Analysis A_nonorm_nobkgd Normalization none [Control Probe Profile] TargetID ProbeID 1.Signal_Grn 1.Signal_Red ... -- 3. By concatenating the sample and control probe files I can feed them to methyLumiR, and the methyData at QC gets set correctly; manually converting the resulting object to a MethyLumiM object seems to be causing trouble downstream through. Trying to directly import the merged data file into lumiMethyR fails again Pointers very much welcome! Best, Oliver > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.0-5 IlluminaHumanMethylation450k.db_1.4.6 [3] org.Hs.eg.db_2.6.4 RSQLite_0.11.0 [5] DBI_0.2-5 AnnotationDbi_1.16.10 [7] lumi_2.6.0 nleqslv_1.9.0 [9] methylumi_2.0.1 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affy_1.32.0 affyio_1.22.0 annotate_1.32.0 BiocInstaller_1.2.1 [5] grid_2.14.0 hdrcde_2.15 IRanges_1.12.5 KernSmooth_2.23-6 [9] lattice_0.20-0 MASS_7.3-16 Matrix_1.0-1 mgcv_1.7-9 [13] nlme_3.1-102 preprocessCore_1.16.0 tools_2.14.0 xtable_1.6-0 [17] zlibbioc_1.0.0 -- Skype: ohofmann Phone: +1 (617) 365 0984 Associate Director Bioinformatics Core Harvard School of Public Health http://compbio.sph.harvard.edu/chb/