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Expression of a gene across all cancer datasets

I want to make a boxplot to show the expression of a gene across different TCGA cancer datasets. Is there any R package for that or Is there any easier way for that? There is an R package RTCGA for that. But only few cancer datasets are available with that.

Do I need to download all the cancer datasets for that?

rna-seq r tcga geneexpression cancer
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updated by GenoMax GenoMax • written by Vasu Vasu

While you wait for an answer see an example using cBioPortal.

You can click on the DATA button in the Expression tab to download the data and plot it any way you want.

Not certain how long the above link will stay valid but you should get page that looks something like this

Capture

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written by GenoMax GenoMax

Thank you. Is that Expression is RSEM counts log scale?

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written by Vasu Vasu

2 answers

The location of expression information has moved to Plot tab. Here is a link to new location (not sure how long the link will stay valid). But should look something like this

cBioPortal

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written by GenoMax GenoMax

Check out the curatedTCGAData package. It brings together a range of different assays (including RNA expression) and let's you work with only what you need, so you don't have to download everything. Levi Waldron has a great walkthrough of how to work with MultiAssayExperiment objects, and particularly highlights the curatedTCGAData package.

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written by mmfansler mmfansler

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