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Should I use z-score in marker expression heatmaps?




Posts: 4

Joined: Wed Nov 21, 2018 4:08 pm

Post Tue Dec 14, 2021 3:30 pm

Should I use z-score in marker expression heatmaps?

Hi all

I am analysing imc data using mainly CATALYST (from Helena Crowell). This package doesn't use z-score until the last heatmap to study differential expression. I am having difficulties to understand when to use the different scaling and transformation options. For instance, in CATALYST I'm trying to understand why the first heatmap uses the scaled median expression, the second the median scaled, the third one the normalize frequency, same for DA heatmap, and the DS heatmap uses the z-normalized expression.

I have special interest for the z-normalized expression because I have been asked to produce every heatmap using z-score. Firstly; How could I do it? I have tried to modify the different heatmaps in CATALYST without success, I have tried scater::plotHeatmap, I have tried singlecellTK::plotSCEHeatmap but it produces a huge vector that my laptop can't handle. Do you have any suggestion to heatmap a (fairly big) singlecellexperiment using z-score?

And secondly; Is there any reason why I shouldn't do it in every heatmap? I guess there is when they don't do it with CATALYST but I need this information if I'm not going to z-score every heatmap. On the other hand, a recent imc paper by A. Rendeiro uses z-score in the heatmap used to identify cell populations.

I am confused and any help will be very welcome.




Posts: 24

Joined: Sun Oct 19, 2014 10:15 pm

Post Fri Dec 17, 2021 6:17 am

Re: Should I use z-score in marker expression heatmaps?

Hi Juan,

Without knowing exactly what's trying to be visualised it is a little hard to say, but different scaling might be used on different heatmap when trying to show different things -- for example if one is showing expression levels of markers, then a simple min/max signal intensity scaling would suffice. If trying to show fold change for populations across experimental groups, then perhaps z-score might be used etc. It's a vague answer I know, but I guess the point is that that different scaling might be appropriate for different purposes.

In terms of help with that specific issue creating that heatmap in CATALYST, you can always submit an 'issue' on their Github: https://github.com/HelenaLC/CATALYST/issues. That way the authors/maintainers can comment directly.

If you want some more flexibility in the way you make heatmaps and how you scale the data, you can also check out our package Spectre (https://immunedynamics.io/spectre/) -- you basically just manage the data as a large table (cells vs markers) and can apply whatever scaling you like, include z-score. Then you can make whatever type of heatmap you like. See a quick tutorial here: https://wiki.centenary.org.au/display/S ... g+heatmaps.

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