Analyzing 450k Methylation from TCGA Website
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@alejandretheodore-7624
Last seen 6.3 years ago
United States

Hi

 

 

 

 

Thank you for taking the time to read this. I am relatively new at programming and bioinformatics, however I am currently working on a project to analyze Illumines 450k methylation idat files from the TCGA website. 

For some reason, when I try to get the Beta Values of a preprocessQuantile mset , The output of getBeta(Mset) when converted to a csv has very poor format.

If anyone has any advice, suggestions, or can help me out It would be amazing and greatly appreciated!

Thank you,

Ted

 

 

minfidata minfi illuminahumanmethylation450k.db illuminahumanmethylation450kanno.ilmn12.hg19 • 1.7k views
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What are you trying to do? What exactly does 'has a poor format' mean?

Please note that asking a very direct and concise question like

'I am trying to output the beta values after quantile normalizing using minfi, as a csv file for further processing, and I would like to have the data in a format like this:'

is much more likely to get a useful response.

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