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Question: DESeq2 lfcShrink with interactions
0
15 days ago by
hannepainter0 wrote:

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.

modified 15 days ago by Michael Love21k • written 15 days ago by hannepainter0
0
15 days ago by
Michael Love21k
United States
Michael Love21k wrote:

There is a section in the vignette where we show how to arrange various contrasts so they are a single coefficient in the design and therefore can be used with apeglm.

Note that ashr can work with a results table alone, so it works already without rearrangement.