Dear Bioconductor Community,
I am using DESeq2 to analyse a mouse RNAseq dataset and have an identical study design to one described in in example section of ?results.I have pasted below:
## Example 3: two conditions, three genotypes # Using interaction terms dds <- makeExampleDESeqDataSet(n=100,m=18) dds$genotype <- factor(rep(rep(c("I","II","III"),each=3),2)) design(dds) <- ~ genotype + condition + genotype:condition dds <- DESeq(dds) resultsNames(dds) # the condition effect for genotype I (the main effect) results(dds, contrast=c("condition","B","A")) # the condition effect for genotype III. # this is the main effect *plus* the interaction term # (the extra condition effect in genotype III compared to genotype I). results(dds, contrast=list( c("condition_B_vs_A","genotypeIII.conditionB") ))
I am specifically interested in looking at the condition effect for genotypes I-III and have adapted the contrasts listed above for my own dataset. However, I am struggling to perform lfcShrink() using types "apeglm" and "ashr".
Does any one have any suggestions on how to perform log fold change shrinkage on this design?
I look forward to your replies.