GEOquery and MethylAnalysis
Entering edit mode
3.2 years ago
alex.v.nesta ▴ 30


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.

R Methylation Methylumi GEO GEOquery • 1.0k views

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