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how can i get normalized gene expression matrix in TCGA?
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2.4 years ago
ghmdsr • 30
@ghmdsr46330

i want to run an algorithm. The algorithm calculates TF activities score per sample,. The algorithm says ' Input needs a normalized gene expression matrix'.

so I tried to get normalized gene expression matrix,

  1. TCGA breast cancer raw count from GDAC.
  2. sample-wise normalization ( TMM/ limma voom transformation)
  3. gene-wise normalization

my question is :

  1. Can i get normalized gene expression matrix in GDAC? Do I have to normalize the raw count manually?

  2. My trying is right? if not, please give me advice.

please help me~~

RNA-Seq gene • 956 views
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2.5 years ago
RamRS 21k
@RamRS

We host a lot of processed data at LinkedOmics, including gene-level normalized RNAseq counts. For TCGA-BRCA, check out http://linkedomics.org/data_download/TCGA-BRCA/

You can access similar data for all TCGA cancer cohorts here: http://linkedomics.org/login.php#dataSource

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2.5 years ago
EagleEye 6.4k
@EagleEye12958

Answer to part of your question:

From this repository you can download archived (2012) normalized data for TCGA pan-cancer RNA-seq in a more convenient way.

If you like to download RPKM normalized data from GDC portal use these filters.

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