differential expression RNASeq DESeq2

Question

[Rob]

I am using DESeq2 for differential expression analysis. I want to account for treatment and Sex. I have the following code. how and where in the code should I add sex?

dds <- DESeqDataSetFromMatrix(countData = rawdata,
                              colData = metadata,
                              design = ~ treatment)

dds <- DESeq(dds)
res <- results(dds)

[ATpoint]

It is generally expected that you read the tools manual first. Even in the "quick start" section there is an example on adding covariates to the design: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Answer 1

[nhaus]

Simply add it in the design formula:

dds <- DESeqDataSetFromMatrix(countData = rawdata,
                              colData = metadata,
                              design = ~ treatment + Sex )

[Rob]

Thank you nhaus Can also this be done for more than 2 covariates? such as: treatment, sex, stage of cancer?

[nhaus]

Yes, you can add it the same way.

[Rob]

Thanks for responding nhaus