I am trying to use RUVr with DESeq2. However, I am not sure how to extract the deviance residuals from the deseq model.

Does anyone know an equivalent method in deseq to the following code using edgeR:

From the RUVseq vignette

design <- model.matrix(~x, data=pData(set))
y <- DGEList(counts=counts(set), group=x)
y <- calcNormFactors(y, method="upperquartile")
y <- estimateGLMCommonDisp(y, design)
y <- estimateGLMTagwiseDisp(y, design)
fit <- glmFit(y, design)

res <- residuals(fit, type="deviance")

The last line is the point in question.

Thank you!