enter code hereHi everyone,
I have 5 control samples and 5 treatment samples for the same patients and I would like to extract the differentially expressed genes between control and treatment samples.
The method I am using now is:
dds <- DESeqDataSetFromMatrix(countData = counts_set,colData = annotation,design = ~ condition) dds <- DESeq(dds) res <- results(dds,contrast=c("condition","Treatment","Vehicle"))
where condition represent control and treatment as follows:
condition 01_C Vehicle 02_C Vehicle 03_C Vehicle 04_C Vehicle 05_C Vehicle 01_T Treatment 02_T Treatment 03_T Treatment 04_T Treatment 05_T Treatment
Could you please let me know if this is a correct way to do?