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Syksy / curatedPCaData

Bioconductor R-package: Curated Prostate Cancer Data
Creative Commons Attribution 4.0 International
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Splitting apart OSF portion of TCGA #18

Closed Syksy closed 2 years ago

Syksy commented 3 years ago

The OSF portion of TCGA data currently breaks the consensus of how each MAE dataset is structured. It should be considered, if the OSF data should be kept along as a separate MAE-entity, harmonizing the presentation of each dataset. Further, the added value of OSF over conventional TCGA dataset should be clearly reported, to avoid i.e. duplication of samples if user uses both datasets.

Syksy commented 3 years ago

OSF: TPM-normalized superior method of normalization CBio's median: Conventional approach but already breaks few assumptions for e.g. few immunedeconv methods (rsam would be the native values)

Syksy commented 2 years ago

We've moved on to using GDC's HTSeq FPKM-UQ instead of OSF dataset.