Hi Mike and community,
I am recently doing DEG analysis by using Deseq2.
I am trying to get differentially expressed genes in African American (AAM) and European American (EAM) prostate cancer populations by using the TCGA dataset.
My target is to see upregulated and downregulated genes in the African American population.
I used the below code to set the level of my population.
As I want to see upregulated genes in African American Males (AAM), is it the right way to set the level? or I have to set the level as ("EAM", "AAM")?
sampledata$Race <- factor(sampledata$Race, levels=c("AAM", "EAM"))``` deseq2Data <- DESeqDataSetFromMatrix(countData=rawCounts_me, colData=sampleData_me, design= ~ Race)