Question: Extract methylation data from a FirehoseData
0
gravatar for carlos.ruiz
4.1 years ago by
Spain/Barcelona/CREAL
carlos.ruiz0 wrote:

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 • 880 views
ADD COMMENTlink modified 4.0 years ago by samur0 • written 4.1 years ago by carlos.ruiz0
Answer: Extract methylation data from a FirehoseData
0
gravatar for samur
4.0 years ago by
samur0
United States
samur0 wrote:

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

 

 

ADD COMMENTlink written 4.0 years ago by samur0
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