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Get an expression table that matches what FoldChange function uses #9376
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Bump - any suggestions is welcome! |
How many samples do you have? For a small number of samples, there is an issue with the added pseudocount |
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 Thank you for answering! |
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.
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