MCPcounter Heat map interpretation

Question

[David_emir]

Hello all,

I am trying to understand the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression data from TCGA and for this, I have used MCPcounter, an R package. Somehow I am not able to understand the Heatmap generated MCPCounter Heatmap. It would be great if you guys let me know how to interpret this heatmap, what correlation can be made out of it.

Thanks a lot for your help,

Sincerely,

Dave

Answer 1

[Kevin Blighe]

Dear Dave,

In the heatmap dendrogram at top are your samples; the dendrogram at right shows different immune cell signatures. In the heatmap itself, blue indicates lower expression of a particular immune cell signature in a particular sample; red indicates higher expression.

Your immune cell signature dendrogram generally appears to be split between B- and T-cells, with varying expression of these in your samples.

Kevin

[David_emir]

Thanks a lot Kevin, for being such a great help!

[Kevin Blighe]

You are very welcome, David!