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Get an expression table that matches what FoldChange function uses #9376

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DelongZHOU opened this issue Oct 8, 2024 · 5 comments
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@DelongZHOU
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Hello,

I want to make sanity checks for the FoldChange of differential expression analysis. At the moment I'm using the output from AggregateExpression to estimate the expression level, but for about 10% of the genes the direction of AggregateExpression and direction of FoldChange do not match.

This is discussed in issue #8682 and I appreciate the argument involving number of cells - but this still doesn't match when I take the average per cell.

In one of my analysis I have a pair of genes showing opposite sign of L2FC, but they both show higher value in treatment vs control for the sum of normalized count (AE over data slot) , and average normalized count (the previous sum divided by number of cells in each condition).

If AggregateExpression is not the best way to get the expression table, which function should I use?

Thank you!
PS, I'm using Seurat 4.4.0.

@DelongZHOU
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Bump - any suggestions is welcome!
Thank you!

@roi-meir
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How many samples do you have? For a small number of samples, there is an issue with the added pseudocount
See this issue for more details - FoldChange results depend on the group size

@DelongZHOU
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I have 3 to 5 / condition x 3 conditions

But you are using Seurat 5.1 and I'm using Seurat 4.4.0, the change in pseudocount behavior happened between the two versions.

@roi-meir
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I missed the version you are using.

Can it be related to the issue mentioned here #6701?
From the documentation, it was fixed by v4.4 but here someone mentions that it wasn't fixed for all cases, so it may be relevant to you.

@cyrillustan
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@roi-meir Thank you for answering!
@DelongZHOU I'll close this for now. You can reopen if you have more questions.

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