Expression of a gene across all cancer datasets

Question

[Vasu]

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?

[GenoMax]

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

[Vasu]

Hi genomax,

I'm not able to find that Data option to download the expression data now. [http://www.cbioportal.org/index.do?session_id=5b9f65a0498eb8b3d567e16f&show_samples=false&clinicallist=CANCER_STUDY%2CPROFILED_IN_MUTATION_EXTENDED]

Could you please have a look what could be the reason for that? Thank you

Answer 1

[GenoMax]

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

Answer 2

[mmfansler]

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.