Should I use z-score in marker expression heatmaps?
Posted: Tue Dec 14, 2021 3:30 pm
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.
Regards
juan
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.
Regards
juan