Dear all,

I believe I have understood now how the grouping of variables work:

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

the condition effect for genotypeIII

results(dds, contrast=c("group", "IIIB", "IIIA"))

My orginal code was:

dds4 <- DESeqDataSetFromMatrix(countData = cts,
                               colData = colData,
                               design = ~ BATCH + AGE + SEX + CONDITION

So if I use above code will my experiment not be controlled for BATCH, AGE and SEX? Or means "design(dds) <- ~ group" that i am adding "group" to " ~ BATCH + AGE + SEX + CONDITION" ... making it " ~ BATCH + AGE + SEX + CONDITION + group"? But then "condition" would be twice kind of in my formula as "CONDITON" and as "group"?!

I am confused, thank you! Bine

So if I use above code will my experiment not be controlled for BATCH, AGE and SEX?

First of all are you sure that you need to control for those? Does, say, a PCA plot show that those are strong contributors to the variation?

If you group doesn't look like paste0(dds$Age, dds$Batch, dds$Sex), then no those elements won't be part of the design if the design is just dds <- ~group.

Or means "design(dds) <- ~ group" that i am adding "group" to " ~ BATCH + AGE + SEX + CONDITION"

If you type design(dds), does it have batch and age and sex in it? If it only says group, then it only has whatever group is.