Extract methylation data from a FirehoseData
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@carlosruiz-8222
Last seen 4.0 years ago
Spain/Barcelona/CREAL

Dear all,

I am using RTCGAtoolbox package to download data from TCGA. Rigth now, I have a FirehoseData object with all the data available and I want to extract the methylation. If I use getData function:

 

 getData(TCGA, "Methylation")

Error in .getListData(object@Methylation, platform) : Please set platform

I have looked up in the documentation and platform is only defined as a list of ids but there are not more clues. There is not information in the vignette either. How can extract methylation data? And, is there any other dataset that requires to set the platform?

 

Thanks,

 

Carlos Ruiz

RTCGAToolbox • 1.0k views
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samur • 0
@samur-7845
Last seen 6.0 years ago
United States

Dear Carlos:

Have you tried to set "patform=1"? Datasets that are originally coming from microarray based platforms are stored in the list and you may need to set list index to get the data. There are several cohorts that you could get microarray expression data from multiple platforms and purpose of index is to export the one you need.

Thanks,

Mehmet

 

 

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