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bioc-context - Bioconductor package research openai/gpt-5.6-luna/medium

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@DESeq2 How does apeglm log2FoldChange shrinkage differ from ashr shrinkage? What is the recommended log2FoldChange shrinkage method? Show source code chunks to compare.

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  • search (In DESeq2 1.52.0, how does apeglm log2FoldChange shrinkage differ fro...)
  • read (vignettes/Analyzing-RNA-seq-data-with-DESeq2.md)
  • grep (source)
  • read (source/R/lfcShrink.R)
  • read (source/man/lfcShrink.Rd)
  • search (apeglm versus ashr shrinkage: prior distribution, posterior estimate,...)
  • read_many (source/R/lfcShrink.R +2 ranges)
  • evidence (vignettes/Analyzing-RNA-seq-data-with-DESeq2.md +6 spans)
  • evidence (reference-manual.md +5 spans)
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Scope

This is for DESeq2 1.52.0 (Bioconductor 3.23). Both estimators are called through lfcShrink().

Aspect apeglm ashr
Prior Adaptive, heavy-tailed Student’s-t prior Fitted mixture of Normal distributions
Input used Count matrix, design matrix, dispersions, offsets, weights DESeq2 MLE LFCs and their standard errors
Point estimate Posterior mode / MAP estimate Posterior mean
Large LFC Heavy tails reduce shrinkage of genuinely large effects Mixture components adapt and avoid excessive shrinkage
Contrasts Not supported directly; requires coef Supported

apeglm re-estimates the coefficient under the negative-binomial count likelihood, whereas ashr treats the estimated LFC and its standard error as an approximately Normal measurement and shrinks it under an empirical mixture prior. [E4] [E7]

Recommended method

For the usual single-coefficient LFC shrinkage, use: 

res <- lfcShrink(dds, coef=2, type="apeglm")

apeglm has been the DESeq2 default since 1.28.0 and is the general recommendation wherever its coef requirement fits. [E6]

4

DESeq2 source code showing the computation

DESeq2 builds the inputs to the external apeglm optimizer from the count data and the fitted model: 

Y       <- counts(dds)
design  <- model.matrix(design(dds), data=colData(dds))
disps   <- dispersions(dds)
mle     <- log(2) * cbind(res$log2FoldChange, res$lfcSE)
 
fit <- apeglm::apeglm(
    Y=Y, x=design, param=disps, coef=coefNum,
    mle=mle, weights=weights, offset=offset,
    method=apeMethod, ...
)
 
res$log2FoldChange <- log2(exp(1)) * fit$map[,coefNum]
res$lfcSE          <- log2(exp(1)) * fit$sd[,coefNum]

apeglm receives the negative-binomial quantities and returns fit$map and fit$sd; DESeq2 converts them from natural-log to log2 scale. [E1] [E2]

5
Sources - Analyzing-RNA-seq-data-with-DESeq2.md:1123-1129 (DESeq2 1.52.0)- reference-manual.md:983-1000 (DESeq2 1.52.0)- lfcShrink.R:118-152 (DESeq2 1.52.0)- DESeq2.Rmd:876-888 (DESeq2 1.52.0)- apeglm.R:64-102 (apeglm 1.32.0)
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clusterProfiler 4.18.0 ↵

Materializing documentation and source…

clusterProfiler/ ├─ README.md index · citation ├─ NEWS.md release notes ├─ reference-manual.md Rd ├─ vignettes/clusterProfiler.md vignette ├─ curated/ 3 docs └─ source/ YuLab-SMU/clusterProfiler ├─ R/enrichGO.R ├─ R/gseGO.R ├─ R/compareCluster.R ├─ man/gseGO.Rd ├─ vignettes/clusterProfiler.Rmd └─ DIRECTORY.md inventory

Installed clusterProfiler 4.18.0

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@DESeq2 @apeglm shrink this interaction coefficient

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Take the coefficient name from resultsNames(dds), then pass it to lfcShrink(). apeglm shrinks a named coefficient, so no contrast is needed. [E1] [E2]

Sources - DESeq2.md:1123-1129 (DESeq2 1.52.0) - apeglm.md:212-228 (apeglm 1.32.0) - lfcShrink.R:118-152 (DESeq2 1.52.0)
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Check this paired bulk RNA-seq limma-voom script. I am unsure duplicateCorrelation is used correctly. Use $biocontext to verify the workflow, then fix the script.

Verifying duplicateCorrelation workflow

The script runs voom once and passes block only to lmFit. limma documents a different order for a paired design, so I will check the versioned source before I change anything.

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@bioc:limma With voom and duplicateCorrelation, what order does limma document for a paired design?

  • search (duplicateCorrelation voom block consensus correlation paired design)
  • read (vignettes/usersguide.md)
  • read (source/R/dupcor.R)
  • evidence (vignettes/usersguide.md +4 spans)

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Sources - usersguide.md:2142-2170 (limma 3.66.0)- dupcor.R:41-96 (limma 3.66.0)- voom.Rd:58-77 (limma 3.66.0)

BioContext evidence retrieved from the versioned limma vignette, reference manual, and source. limma runs voom twice: once to get weights for duplicateCorrelation, then again with the consensus correlation.

Applying the smallest correction:

v <- limma::voom(dge, design, plot = FALSE)
 
corfit <- limma::duplicateCorrelation(
  v,
  design = design,
  block = sample_info$subject
)
 
v <- limma::voom(
  dge,
  design,
  plot = FALSE,
  block = sample_info$subject,
  correlation = corfit$consensus.correlation
)
 
fit <- limma::lmFit(
  v,
  design,
  block = sample_info$subject,
  correlation = corfit$consensus.correlation
)
 
fit <- limma::eBayes(fit)

The focused test checks that the paired block is retained, the consensus correlation is finite, and the fitted model keeps every coefficient in the design.

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