[BioC] Analysing grouped datasets in repitools
Andrew Beggs [guest]
guest at bioconductor.org
Mon Mar 4 16:48:30 CET 2013
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?
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
 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:
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
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