Dear all,

I have the following problem: I have my model (controlling for Batch, Age, Sex) and I am interested in the condition.

dds <- DESeqDataSetFromMatrix(countData = cts,
                               colData = colData,
                               design = ~ BATCH + AGE + SEX + CONDITION

Now I need to do some grouping the condition, following vignette with

dds$group <- factor(paste0(dds$genotype, dds$condition))
design(dds) <- ~ group

But doing it this way I remove the control for Batch, Age and Sex.

How can I control for all these factors and do the grouping as well?

Thank you very much!

Bine

Note: It's not great to separate all the support site posts that are related to the same analysis. Makes it hard for others to follow your threads.

If your design is not confounded (e.g. you have balanced your conditions of interest within batches or other nuisance variables) then you can do, e.g. ~batch + condition or ~batch + nuisance1 + nuisance2 + condition.

However, if you design is confounded (e.g. there are linear dependencies between the batch/nuisance variables and your condition), then you will encounter an error, in this case you should consult a statistician for resolving this in future datasets.