how can i get normalized gene expression matrix in TCGA?

Question

[ghmdsr]

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~~

Answer 1

[Ram]

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

Answer 2

[EagleEye]

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.