PANCAN RNA-seq normalization

[bilal...@gmail.com]

Hello,

For the PANCAN gene expression data set how was the RNAseq data processed and normalized?

Thanks!

Erhan

[Mary Goldman]

Hi Erhan,

You can always find more information about each dataset by clicking Tools -> About dataset.

For the PANCAN gene expression dataset, we combined all the data from all the TCGA cohorts. This data is mean normalized across the entire cohort in the visualization (https://genome-cancer.ucsc.edu/proj/site/help/#Normalize_columns). Each individual cohort was Level_3 Data (file names: *.rsem.genes.normalized_results), all of which were downloaded from TCGA DCC and then were log2(x+1) transformed.

The PANCAN AWG gene expression was downloaded from SAGE. More information about their normalization and processing can be found there (https://www.synapse.org/#!Synapse:syn1715755).

Best,
Mary
-------------
Mary Goldman
UCSC Cancer Browser
https://genome-cancer.ucsc.edu/

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