Question: DESeq2 log-fold change shrunk to -0.4 instead of zero. Why? · Biostar

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Question: DESeq2 log-fold change shrunk to -0.4 instead of zero. Why?

I'm using DESeq2 to analyze differential gene expression between two groups. As I understand, the log fold changes for genes with low counts (low mean expression) should be shrunken toward zero, but in the MA-plot (which I'm having trouble posting), they're shrunken toward -0.4 or so. Why is this so and how can I fix it? I'm worried all my LFC estimates are off. Thanks.

MA plot

Also posted on Bioconductor: https://support.bioconductor.org/p/90380/

rna-seq deseq2

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written 9.6 years ago by lostisle •

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