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