The vignette of MethyAnalysis package needs to be further improved. I
will update it within next couple of weeks when I have time.
As for creating MethyGenoSet objects, you can either use
MethyGenoSet() function or converted them from MethyLumiM objects
using MethyLumiM2GenoSet function, which is what I use. Basically the
work flow is preprocessing the methylation data in the lumi package
and then converted it as MethyGenoSet class and do further analysis.
Since the MethyAnalysis package is designed for chromosome location
based analysis, 450k data or sequencing data is recommended. 27K data
can still use some functions (like plotting the data) in the package,
but other functions (like slidewindow differential methylation
detection) is not useful for 27k data.
Hope this is helpful to you.
On Wed, Jan 16, 2013 at 8:34 AM, Ranya [guest] <guest at="" bioconductor.org=""> wrote:
> I have successfully installed MethyAnalysis and I am not
understanding how to load my data. The exampleMethyGenoSet RDA file
doesn't give me too much information as to how I need to setup my own
data. I am also unsure if this package is meant for the Illumina 450K
microarray or the 27K.
> -- output of sessionInfo():
> Sent via the guest posting facility at bioconductor.org.