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waldronlab / curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
https://bioconductor.org/packages/curatedTCGAData
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Methylation data platform #49

Closed fedenichetti closed 2 years ago

fedenichetti commented 2 years ago

Hi there, one simple question on methylation data downloaded from the package:

some tumor types have only one Methylation file without a specified platform (e.g. PAAD has only PAAD_Methylation-20160128), while others (like LUAD) have more than one (e.g. LUAD_Methylation_methyl27-20160128 and LUAD_Methylation_methyl450-20160128).

In cases like PAAD, which one should I assume it to be, 450 or 27?

Thanks!

LiNk-NY commented 2 years ago

Hi Federico, @fedenichetti

The data from curatedTCGAData is based on the outputs of RTCGAToolbox. The getLinks function will show data files. It seems like these file names were lost somewhere along the pipeline and should be included in the metadata. 

> RTCGAToolbox::getLinks("PAAD", Methylation=TRUE)
                                                                                                                                                              href 
"gdac.broadinstitute.org_PAAD.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz"
fedenichetti commented 2 years ago

Many thanks!