Question: Analysing grouped datasets in repitools
6.7 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hi I have some Affymetrix tiling arrays from a meDIP (i.e. consisting of a _me and _in files for each sample) experiment I have successfully managed to import into Aroma/repitools. I would like to analyse them as a between group comparison, i.e. I would like to compare differential methylation between the two groups and come up with a top list of differentially methylated probes, with levels of significance. Normally I would do this with limma, but I can't see how this would fit into the data structures produced as part of repitools. Could anyone possibly give me some pointers? BW Andrew -- output of 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 -- Sent via the guest posting facility at bioconductor.org.
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