DESeq2 - shrunken LFC calculation
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@alexandrgopanenko-11598
Last seen 6 months ago

Hello everyone!

I want to ask a question regarding the usage of shrinkage estimators in the frame of differential expression and translation efficiency analysis with DESeq2.

I have to analyze RNA-seq and polysome profiling (or Ribo-seq) datasets in two conditions (e.g. KD vs NORMA).

I used the formula below:

ddsFull <- DESeqDataSetFromMatrix(countsData, colData, design = ~ assay + condition + assay:condition).

dds <- DESeq(ddsFull, test = "LRT", reduced = ~assay + condition).

Next I want to calculate shrunken LFC values:

resultsNames(dds) "Intercept" "assay_rna_seq_vs_ribo_seq" "condition_KD_vs_N" "assayrna_seq.conditionKD"

res_LFCshrinken <- lfcShrink(dds, coef=?, res = res_unshrinken, type="apeglm").

The question is what coef should I use? Could you please explain how to deal with coef parameter?

Thank you in advance, Alexandr

apeglm DESeq2 • 199 views
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@mikelove
Last seen 2 days ago
United States

Take a look first at the vignette. It talks about this at length.

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