disagreement between log2FoldChange and lfcMLE in DESeq2
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aec ▴ 90
@aec-9409
Last seen 4.4 years ago

Dear all,

I am using DESeq2 for a design ~PAIR+GROUP and I obtained for geneX this result:

 

  geneX
baseMean 62.2087194
log2FoldChange -0.33167142
lfcMLE -2.32040851
lfcSE 0.07892334
stat -4.20245054
pvalue 2.64E-05
padj 0.06846016

 

The normalized counts by DESeq2 are these:

 

  geneX
groupB 17.51
groupB 13.94
groupB 31.76
groupA 82.32
groupA 81.39
groupA 146.33

 

Why is it that the log2FoldChange is so different from the lfcMLE? The gene is clearly down-regulated in groupB by a factor>2 and this is not reflected in the log2FoldChange.

deseq2 log2fc shrinkage • 1.5k views
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@mikelove
Last seen 1 day ago
United States

You may be using an older version of DESeq2? The latest version (1.18) doesn't perform LFC shrinkage automatically, but only after running the command lfcShrink(). In addition, the latest version has new estimators which tend to shrink less than the originally proposed shrinkage estimator in DESeq2. Shrinkage is useful for ranking and visualization, but on some datasets, with a particular distribution of underlying LFCs, we found the original shrinkage estimator to be too strong. This could be the case here as well.

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Mike I am using version DESeq2_1.10.1, is it too old?

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That version is from 2 years ago. I'd recommend -- if you're on a laptop, or have permissions to do so -- download the latest version of R and update your Bioconductor packages (unless you need to stick with the 2 year old version for some reason, ... e.g. an ongoing project where you need to continue working with an old set of packages).

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