Correct Data from TCGA for EdgeR Analysis
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3.1 years ago

Hi All,

I am down loading data from cBioportal for and RNA-Seq analysis project. I would like to use EdgeR to measure differential gene expression from the TCGA data sets. When I unpack the tarball file from the cBioportal down load I see 3 different RNA-Seq data sets. They are listed as...

data_RNA_Seq_v2_expression_median.txt data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt data_RNA_Seq_v2_mRNA_median_Zscore.txt

I know EdgeR needs raw counts to do its differental expression analysis. So the Zscore normalized data is out.....Is that correct? Can the data_RNA_Seq_v2_expression_median.txt be used for EdgeR? Or does a more raw read count data set need to be used?

Best,

Joe

rna-seq • 792 views
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