I'd like to analyze the RNA level of TCGA data.
However, there are two categories of the data
One is harmonized data, under this, you can choose the category of "transcriptome Profiling", and then "Gene Expression Quantification", and choose "HTSeq". Basically speaking, only one set of data for each cancer type.
Another is Legacy data, under this one, you can choose the category of "Gene Expression", and then further choose which RNA-seq/microarray chip. There are multiple sets of RNA data that you can choose for a single cancer type.
What's the difference between the two categories of RNA data?? Which one is better??
I think that the "legacy" gene expression data refers to the original processed data (the gene expression analysis methods, genome reference and gene models used may differ between cancer types/projects). The harmonized data was produced by the GDC by reprocessing the data using a single analysis pipeline.
More: https://gdc.cancer.gov/about-gdc/gdc-faqs#
Cheers.
More info about the harmonization process in TCGA:
https://gdc.cancer.gov/about-data/gdc-data-harmonization
https://gdc.cancer.gov/content/gdc-data-harmonization-pipeline
You have some tools/platforms that are adapted to deal with both sources of data, as TCGAbiolionks or Cancer Genomics Clouds (apart from GDC of course):
http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html
https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html
https://docs.cancergenomicscloud.org/docs/about-datasets
There is also an interesting web page and article (TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages (Silva et al. 2016)) that give orientations to retrieve and analize the data using different tools:
https://dockflow.org/workflow/tcga
Hope this helps!
Best regards
A nice relevant paper:
Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data - PMID: 31344359.
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