Extract the Z-score

Support Questions
1

Is there a way to extract the Z-score data from the violin plot for statistical calculations?
Thank you.

2

Hi Haruki,

That’s a great request!

Right now, I’m afraid that it’s not possible to extract the z-score data from the violin plot.

The workarounds I can think of are:

  • You could download the Seurat object (using the ‘Download’ button in the Data Management module) and then calculate the z-score outside of Cellenics.
  • You could download the normalized expression matrix from the Plots and Tables module and the calculate the z-score outside of Cellenics.

Thanks for the feature request!

3

Thank you, Vicky!
I think the Y-axis of the violin plot used to be “normalized expression”, is this the same as the current Z-score?

4

Hi,

There are two options for presenting the data in the violin plot, which can be found under the “Data Transformation” sub-menu:

  • The “Raw values” actually refers to log-normalized expression values. We realise that this is a bit misleading and we’ll work to improve the text here.
  • The other option is the Z-score.