Oncoprinter
Alhawaj, Ali
Hello,
I have a couple of questions about Oncoprint tool.
What does the value in the Heatmap refer to? I’m trying to integrate my RNAseq expression counts with the mutations, and I have a gene matrix count of samples x genes. However, the Heatmap data format asks for a single expression value per sample. Could you please explain the input to me?
Also, After generating my genomic alterations table, the bars look deformed (pic below). Could you help me fix this?
Many thanks!
Ali Alhawaj
PhD student
Cancer department
UCL
David Higgins
Hi Ali,
The “Heatmap” tool in Oncoprint (under “Add Tracks -> Heatmap”) adds an additional track to Oncoprint with gene expression data. The data is presented as a colored heatmap representing a range of values. The values themselves are expression Z-scores that have been normalized within the study. More details are included in our FAQ page, here. The counts of genes themselves are available under the “Download” tab, at the far right of the Query results.
I don’t think I’ve seen Oncoprint look like you’ve shown it in the image. Could you provide more details so we can try to recreate it? What study were you working in? What actions did you perform to make the bars appear that way? What internet browser and operating system are you using on your machine? Please Reply All so that our continued conversation is captured on the cBioPortal Google Group.
Best,
David M. Higgins, Ph.D. | (he/him)
Informatics Program Manager
Center for Data-Driven Discovery in Biomedicine (D3b)
Children’s Hospital of Philadelphia, USA
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