Hello, Apologies if this is a basic question, but I am trying to use the relevel. But the result i.e the number of DEGs does not change before and after the relevel
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~mutant_stat+sex+age+survival) resultsNames(dds) #wt_vs_mut
So, it is wildtype change when compared to mutant. Now, when i relevel such that expression change in mutant (mut) is compared to wildtype(wt)
dds$mutant=relevel(dds$mutant,ref="wt") #relevel so that the level of reference is wildtype
Now, I run deseq2 again and check if the level has been reflected
dds <- DESeq(dds) #run again on relvelled data resultsNames(dds) #mutant_mut_vs_wt
So, yes this time it is mutant vs wildtype. But the number of DGEs does not change between the pre and post relevel. Why, is it so because i assumed that if I change the level for which comparison is happening, DEGs change.
FYI wt,n=700 mut, n=50
I may be missing something here, kindly help?