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Question: how can i get normalized gene expression matrix in TCGA?
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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~~

ADD COMMENTlink 18 months ago ghmdsr • 30 • updated 18 months ago Biostar 20
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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

ADD COMMENTlink 18 months ago RamRS 21k
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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.

ADD COMMENTlink 18 months ago EagleEye 6.4k

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