TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
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@salvocomplicazioni1-14125
Last seen 24 days ago
Germany

I'm trying to analyze TCGA RNA-seq data, so i used TCGAbiolinks, I arrived at normalization data step and i obtained normalized counts matrix, How can I change Ensemble gene name into common gene name?

tcgabiolinks grch38 annotation • 2.6k views
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biomiha ▴ 20
@biomiha-11346
Last seen 5 months ago
UK/Cambridge

I would use biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html)

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@tiagochst-7121
Last seen 18 months ago
Miami, US

You have the names inside the SummarizedExperiment object.

 

An example is in this gist:

 

For hg38 the gene names are retrieved with

values(data)$external_gene_name

 

For hg19 

values(data)$gene_id

 

Where data is the summarizedExperiment object, this data was created using biomaRt.

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