I'm pretty new to bioinformatics in general, and I'm looking for some help.
My Goal: Align a bunch of methylation data each other and look at changes in methylation pattern.
The data set I want to do this with can is found on GEO as "GSE30654"
I'd like to download the package with GEOquery and visualize methylation data of the X chromosome.
So far, I think the package methyAnalysis will allow me to visualize the methylation data all lined up, but I am having trouble getting the GEOquery data in the format that methyAnalysis will accept.
Additionally, I believe that Differentially Methylated Region analysis still needs to be performed on this data set, but I can't get the GEOquery data in a format to do that with DMRcate either.
If I could just get the .idat files from this GEO entry I found a workflow that I can use, but since it is a whole bunch of different samples, I don't think I can easily get the idat files.
To Summarize: 1) How do I convert (Coerce) GEOquery data (Specifically GSE30654) to methylumi so that I can use it with downstream analysis applications. 2) Is it possible to get the .idat files as well as the "Sample_Sheet.csv" from GSE30654
Thanks for your help.