PS Here is my sessionInfo() > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit)
locale:  LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C  LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8  LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0  BiocInstaller_1.8.3  biomaRt_2.14.0  preprocessCore_1.20.0  limma_3.14.4  GenomicFeatures_1.10.2  AnnotationDbi_1.20.5  Biobase_2.18.0  gsmoothr_0.1.5  Repitools_1.4.0  GenomicRanges_1.10.7  BiocGenerics_0.4.0  aroma.affymetrix_2.8.0  affxparser_1.30.2  aroma.apd_0.2.3  R.huge_0.4.1  aroma.light_1.28.0  aroma.core_2.8.0  matrixStats_0.6.2  R.rsp_0.8.2  R.devices_2.1.3  R.cache_0.6.5  R.filesets_2.0.0  R.utils_1.19.5  R.oo_1.11.7  affy_1.36.1  IRanges_1.16.6  R.methodsS3_1.4.2 loaded via a namespace (and not attached):  affyio_1.26.0 Biostrings_2.26.3 bitops_1.0-5 BSgenome_1.26.1  DBI_0.2-5 digest_0.6.3 edgeR_3.0.8 parallel_2.15.2  PSCBS_0.30.0 RCurl_1.95-3 Rsamtools_1.10.2 RSQLite_0.11.2  rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 XML_3.95-0.1  zlibbioc_1.4.0 On Monday, March 4, 2013 3:24:13 PM UTC, Andrew Beggs wrote: > > Hi > > I have multiple Affy methylation tiling arrays, (i.e. _me and _in) arrays > which have been sorted into functional groups, i.e. group 1 (cancer), group > 2 (cancer) and group 3 (normal) > > I normally run Illumina arrays for methylation and so I'm not massively > confident with this platform. I've managed to import my arrays in, and > analyse them with regionStats. > > What I want to do is try a probe level comparison of the three groups, > i.e. group 1 vs. group 2; group 1 vs. group 3 and group 2 vs. group 3 for > significance, i.e. I need a coefficent and p-value. > > I would normally use limma to construct a model, but I can't see how limma > could be applied to the dataset output by regionStats > > Has anyone any experience with his? > > BW > > Andrew > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to email@example.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.