Question: Expression of a gene across all cancer datasets
2
gravatar for Vasu
10 months ago by
Vasu330
Vasu330 wrote:

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?

ADD COMMENTlink modified 10 months ago by mmfansler310 • written 10 months ago by Vasu330
3

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

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax68k

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

ADD REPLYlink written 9 months ago by Vasu330
0
gravatar for mmfansler
10 months ago by
mmfansler310
MSKCC | New York, NY
mmfansler310 wrote:

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.

ADD COMMENTlink written 10 months ago by mmfansler310
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2172 users visited in the last hour