lfcshrink() and 2 conditions, 3 genotypes
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Entering edit mode
Nayrouz • 0
@ea088d93
Last seen 10 months ago
Canada

Hello,

How could I use the lfcshrink() function when I need to examine the condition effect on genotype III?

results(dds, contrast=list( c("condition_B_vs_A","genotypeIII.conditionB") ))

I tried the below code but I got an error.

lfcShrink(dds, contrast = list(c("condition_B_vs_A", "genotypeIII.conditionB")))
#Error in lfcShrink(dds, contrast = list(c("condition_B_vs_A", "genotypeIII.conditionB")),  : 
 #type='apeglm' shrinkage only for use with 'coef'
lfcshrink DESeq2 • 666 views
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Entering edit mode
@mikelove
Last seen 16 hours ago
United States

First, read over the section on the vignette that addresses this, in the Extended section on shrinkage estimators. Easiest would be to use ashr.

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