lfcshrink() and 2 conditions, 3 genotypes
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Entering edit mode
Nayrouz • 0
@ea088d93
Last seen 24 days 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 • 102 views
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Entering edit mode
@mikelove
Last seen 1 day 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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