Hi all, I've question regard dmpFinder method in Minfi package 1.10.2. My Dataset has composed by 49 Samples. I've splitted my methylation profiling matrix (always SWAN normalized, filtered on p-value and sex chromosomes) with all Cg Probe ID, in some sub-matrices with Cg Probe ID that covering some genomic regions of interest. Then I call dmpFinder method with a sub-matrix as input. I got strange results from dmpFinder like this (only the head of dmp result table): intercept f pval qval 63803 -1.7708894377 33.0502014338 5.7429067504821e-07 0.0295814503 35558 -2.0594919426 30.5216185561 1.26280541394315e-06 0.0325232649 37196 1.6545682828 29.0969331518 1.99216453478782e-06 0.0342051617 17326 2.6031068482 24.9262239789 7.98412955973361e-06 0.1028147164 13446 2.0077186022 22.9217904185 1.60468187115676e-05 0.1233703844 21260 -1.6861162973 22.9201474848 1.60561441086618e-05 0.1233703844 54663 -2.2310293103 22.4803114045 1.87681049414807e-05 0.1233703844 9834 -0.9628830679 22.2169618742 2.06170232814137e-05 0.1233703844 2522 -1.7629900864 22.0160423365 2.2154998438435e-05 0.1233703844 As you have to see the Cg Probe ID is strange/non-usual (It seems truncated), Why? What's happened? A sub_matrix is like this (only its first rows) and it has less than one hundred thousand rows: Sample_1 Sample_2 Sample_3 ... Sample_49 cg04761824 -2.2724251241 -1.135988521 -1.4793999396 ... ... cg13965272 -2.151897009 -1.214990173 -2.0012750288 ... ... cg14138549 -1.2409738471 1.4247978635 0.0392966574 ... ... cg14585967 -2.2641519697 -1.5533007179 -3.0725520279 ... ... cg14631486 -2.0956352791 -1.0406844361 -2.2111675268 ... ... cg00557872 2.5607532507 0.7251602564 1.5072624496 ... ... cg02570981 -2.1684190566 -1.0676436576 -1.6305898233 ... ... cg03836638 0.5482586716 -0.3210537101 0.8483187571 ... ... cg04267704 -2.6055084465 -3.0680224081 0.2251577771 ... ... Thanks in advance, Giovanni Laboratory of Preclinical and Translational Research IRCCS - CROB Oncology Referral Center of Basilicata Rionero in Vulture - Italy ***** sessionInfo ***** > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] minfi_1.10.2 bumphunter_1.4.2 locfit_1.5-9.1 [4] iterators_1.0.7 foreach_1.4.2 Biostrings_2.32.1 [7] XVector_0.4.0 GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 [10] IRanges_1.22.9 lattice_0.20-29 Biobase_2.24.0 [13] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] annotate_1.42.1 AnnotationDbi_1.26.0 base64_1.1 [4] beanplot_1.1 codetools_0.2-8 DBI_0.2-7 [7] digest_0.6.4 doRNG_1.6 genefilter_1.46.1 [10] grid_3.1.0 illuminaio_0.6.0 limma_3.20.8 [13] MASS_7.3-33 matrixStats_0.10.0 mclust_4.3 [16] multtest_2.20.0 nlme_3.1-117 nor1mix_1.1-4 [19] pkgmaker_0.22 plyr_1.8.1 preprocessCore_1.26.1 [22] RColorBrewer_1.0-5 Rcpp_0.11.2 registry_0.2 [25] reshape_0.8.5 R.methodsS3_1.6.1 rngtools_1.2.4 [28] RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0 [31] stats4_3.1.0 stringr_0.6.2 survival_2.37-7 [34] tools_3.1.0 XML_3.98-1.1 xtable_1.7-3 [37] zlibbioc_1.10.0 > ***** End sessionInfo ***** [[alternative HTML version deleted]]