PS Here is my sessionInfo()
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
[2] BiocInstaller_1.8.3
[3] biomaRt_2.14.0
[4] preprocessCore_1.20.0
[5] limma_3.14.4
[6] GenomicFeatures_1.10.2
[7] AnnotationDbi_1.20.5
[8] Biobase_2.18.0
[9] gsmoothr_0.1.5
[10] Repitools_1.4.0
[11] GenomicRanges_1.10.7
[12] BiocGenerics_0.4.0
[13] aroma.affymetrix_2.8.0
[14] affxparser_1.30.2
[15] aroma.apd_0.2.3
[16] R.huge_0.4.1
[17] aroma.light_1.28.0
[18] aroma.core_2.8.0
[19] matrixStats_0.6.2
[20] R.rsp_0.8.2
[21] R.devices_2.1.3
[22] R.cache_0.6.5
[23] R.filesets_2.0.0
[24] R.utils_1.19.5
[25] R.oo_1.11.7
[26] affy_1.36.1
[27] IRanges_1.16.6
[28] R.methodsS3_1.4.2
loaded via a namespace (and not attached):
[1] affyio_1.26.0 Biostrings_2.26.3 bitops_1.0-5
BSgenome_1.26.1
[5] DBI_0.2-5 digest_0.6.3 edgeR_3.0.8
parallel_2.15.2
[9] PSCBS_0.30.0 RCurl_1.95-3 Rsamtools_1.10.2
RSQLite_0.11.2
[13] rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 XML_3.95-0.1
[17] 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
>
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