I have 4 tissue types which I am trying to contrast between different groups using DeSeq2 in order to find genes unique to each tissue type(Let's say tissueA vs all others). I went through some posts: https://support.bioconductor.org/p/86347/ and https://www.biostars.org/p/317843/ and tried the numeric contrast option.
dds_test <- DESeq(dds_gene) results(dds_test, contrast = c(1, -1/3, -1/3, -1/3))
As, I did not fully understand which number referred to what condition, and tried using the list form in contrast but the commands were throwing an error. I went through the post https://support.bioconductor.org/p/105087/ and tried to follow the same.
dds_test2<- DESeq(dds_gene, betaPrior=T) resultsNames(dds_test2)  "Intercept" "tissueA" "tissueB" "tissueC" "tissueD" results(dds_test2, contrast = list(c("tissueA"),c("tissueB","tissueC","tissueD")), listValues=c(1, -1/3))
This resulted in completely different outputs. Then I tried to check the previous design resultnames using the resultsNames(dds_test) command which showed the following output:
 "Intercept" "tissue_B_vs_A" "tissue_C_vs_A" "tissue_D_vs_A"
What is the difference between the two approaches? Which way is the correct way of doing this? Have I misinterpreted something?