HeatMap calculations and display in EnrichmentMap

[geoffre...@gmail.com]

Sorry if these questions have been asked before, but I could not find reference by searching previous posts.

I have invoked the EnrichmentMap app from within GSEA, ie by pointing to a GSEA results folder. I am using GSEA v3.08, Cytoscape 3.30 and EnrichmentMap v2.1, running on Windows 7 Professional SP1 with Java 1.8.0_151. I have 64GB RAM and using 64-bit version of Java.

I am asking whether the heatmap display in the Table view can be modified with respect to the range of values displayed and the potential to use other color schemes.

1. In the EnrichmentMap Table view there is the option to show row normalized data. The manual indicates the values represent mean-subtracted and divided by standard deviation, commonly known a z-score.

However, these values do not match the z-score values that I calculate in external software. Typically the normalized values in the heatmap view are much greater in range than those I have calculated separately. This leads to very weak looking heat maps in the Table view.

Am I misunderstanding the normalization calculation?

2. Is there a way to modify the range or the colors displayed in the heatmap legend? I have not found any reference to that in the user guide, except that the range will vary based on different data sets.

3. A row normalization from zero to one would be helpful. This is the customary display in the GSEA heatmap settings.

A final comment, I really appreciate this heat map view which shows the complete data set, and not just the paired comparison performed. It also provides a very helpful and dynamic way to explore the Gene Sets enriched as well as the genes within the gene sets. So, I want to also say thanks for all the development done so far.

[Ruth Isserlin]

Hi,
Firstly, you are using an old version of EM. Any chance you can update to the latest version. We have fixed quite a few bugs and issues since that release.
1. yes. As stated in the manual we are calculating the z-score for each value. With regards to your comparison to an external method, in the expression viewer do you have data for one or two datasets? In the older version of EM I believe it calculated the row norm across all the data as opposed to by dataset so if you have more than one dataset the values will be effected by the other dataset. (this has been corrected in the current release though).
2. Unfortunately not but you can download the data in the heat map for the subset selected to a text file and create your own heat map with your program of choice and truthfully that is what I often do when generating specific heat map for figures and stuff.

Thanks,
Ruth

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