Question: Methylation statistical analysis
1
gravatar for dBlandford
3.5 years ago by
dBlandford20
Israel
dBlandford20 wrote:

So I've been given a JMP file containing methylation percentage data for a few subjects. The file is organized by columns, containing the chromosome number, position on chromosome, and percentage of methylation for that location for each subject (15 subjects total).

chr pos subj
chr1 10485 9.2208

I tried going over a few bioconductor packages for R as well as different software for methylation analysis, but found no one that can handle this kind of data. The purpose is to run an analysis (similar to a gwsa using Plink, for exmaple) in order to find differences in methylations between the study groups.

Any advice on either how to organize the file to a more proper file format or which software will be appropriate for the situation?

Thanks.

ADD COMMENTlink modified 3.5 years ago by Sean Davis25k • written 3.5 years ago by dBlandford20
2

Was the source of this data a methylation array or something else? You'll almost always have better luck with the raw data rather than something that someone exported from JMP.

ADD REPLYlink written 3.5 years ago by Devon Ryan89k
1
gravatar for Sean Davis
3.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You could take a look at the limma package, as it handles differential methylation (similar to gene expression).  Alternatively, take a look at Bumphunter.  

As for data format, you can load the data into R and simply manipulate it there into the data structure as needed.

ADD COMMENTlink written 3.5 years ago by Sean Davis25k
1

Note that data should be logit transformed for use in limma (or pretty much anything else).

ADD REPLYlink written 3.5 years ago by Devon Ryan89k
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