how to download "TCGA RNA Seq V2 RSEM" full table

[Tang, Xing (xing)]

Hi,

 

I want to perform clustering analysis of patients and genes based on the z-score cbioportal has provided. However, they only provide download by each gene. I further checked https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm. This website provides only expression profile instead of z-score. Is there  a way that I can download z-score for all genes? Thanks!

 

Xing Tang

 

[JianJiong Gao]

Hi Xing,

The z-scores were calculated by our in-house procedure, but currently
we are not providing batch download for our datasets. Sorry about
that. They maybe available for download on the cBioPortal in the
future. For the moment, you could download the data from TCGA data
portal or Broad Firehose (http://gdac.broadinstitute.org/) and
calculate the zscore with your own script.

Best,
-JJ

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[russ....@gmail.com]

Hi,

I wanted to bump this thread and see if there has been any movement towards providing a direct download of these data. Across the various listservs it seems that quite a lot of people are interested in these data, and recalculating these values by hand would require a bit of effort even for an experienced computational biologist. Is there a repository of the z-scores somewhere?

-Russ