Discrepancy in expression values between VIP and CellXGene

interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

https://cellxgenevip-ms.bxgenomics.com

MIT License

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Discrepancy in expression values between VIP and CellXGene #41

Closed ShanSabri closed 3 years ago

ShanSabri commented 3 years ago

Hi, I'm noticing that the expression range seems to differ between CellXGene and the VIP plugin.

In the example dataset (https://cellxgenevip-ms.bxgenomics.com) it looks like CD79A has a max normalized expression of 7.485:

But when I plot the distribution of this gene across clusters I see that the y-axis is capped at 20:

How is this 20 computed? Also what does the Expression cutoff: field correspond to? How can I get these values on the same scale?

interactivereport commented 3 years ago

Please change "Scale data ... ..." option to "No".

ShanSabri commented 3 years ago

Perfect - thank you!