Where to download expected counts instead of normalized RSEM for TCGA LUAD?
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Ahdee ▴ 50
@ahdee-8938
Last seen 18 days ago
United States

Dear all, this is not a typical R question but I'm wondering if anyone knows a url or even a package that can download expected_counts for the TCGA data like LUAD.  I can easily download the rsem gene normalize dataset from places like firehose however I need to run a DGE using something like edgeR or Voom - limma that would require the counts instead.  Does anyone have a source? 

thanks. 

 

limma tcga • 727 views
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@steve-lianoglou-2771
Last seen 15 hours ago
Denali

Here are some options:

  1. Get the data from this paper, where the reprocessed the TCGA RNA-seq data using subread (GEO link).
  2. The recount project has a reprocessed version of the TCGA data. Click on the TCGA tab at the top there.
  3. The ARCHS4 project provides the "recount"ed TCGA data as and HDF5 file on its downloads page. This may be a more palatable way to consume the entire TCGA data, depending on how you plan on using it.
  4. The toil project has a subset of the TCGA data reprocessed using kallisto. You should be able to chase down a way to download the data from there, or from its listing on the kallisto site.
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Steve, thanks, this is perfect.  the recount2 project looks awesome.  On top of that there is a R packages to make the download easier.  Found a great tutorial here in case anyone else is interested. 

https://www.bioconductor.org/packages/devel/workflows/vignettes/recountWorkflow/inst/doc/recount-workflow.html

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