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
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-8LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8LC_MESSAGES=en_GB.UTF-8
You are correct. regionStats was not designed to look at individual probes.
First, you need to do MAT normalisation on your arrays. This is implemented in
aroma.affymetrix. Then, you extract the normalised values into a matrix.
extractMatrix will do this. You can then create a model matrix and
