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What's the difference between between average expression and average expression scaled>

In R/Seurat, I'm looking at the expression of genes, for example Ddx4. I created a dot plot and then looked at the data behind the dot plot. There's average expression and average expression scaled. What's the difference? Which one should I consider for seeing if the gene is expressed or not? I also don't understand why average expression scaled has negative values as how can a gene be negatively expressed? Sorry if this is a really basic question I'm in undergrad and don't know anything.

example data here

seurat
• 2,349 views • link
written by Dog • Dog

1 answer

It is what is says, the scaled values, so the average expression transformed to Z-scale. Code:

values <- c(3.12, 5.18, 4.18, 0.53, 0.24, 0.7, 0.2, 0.34, 0.399)
scale(values)
[1]  0.7500091  1.8041498  1.2924310 -0.5753425 -0.7237409 -0.4883503 -0.7442097 -0.6725690 -0.6423776

It's a measure of relative (standardized) change: https://en.wikipedia.org/wiki/Standard_score

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written by ATpoint ATpoint

so how does negative expression work? Should I look at average expression or scaled avg expression to see if a gene is actually expressed?

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written by Dog • Dog

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