I have a dds object with these coldata:
> head(colData(dds_RNA)) DataFrame with 6 rows and 9 columns Sample Subject Batch Generation Genotype Area Sex Group sizeFactor <character> <character> <factor> <numeric> <character> <character> <factor> <factor> <numeric> 2B2 2B2 2B2 A 244 TT ACB F NACTT 0.530504 3B1 3B1 3B1 A 243 CC ACB M NACCC 0.701971 3D1 3D1 3D1 A 244 TT ACB M NACTT 0.617343 3E2 3E2 3E2 A 244 TT ACB F NACTT 0.844923 4B2 4B2 4B2 A 251 CC ACB F NACCC 1.004906 4C3 4C3 4C3 A 252 CC ACB F NACCC 0.848526
But if I do
> resultsNames(dds_RNA)  "Intercept" "Group1" "Group2" "Group3" "Group4" "Group5" "Sex1" "Batch1" "Batch2" "Batch3" "Batch4"
I don't understand why. I was used to see that it would give me Group_NACTT_NACCC options, and I have no clue why it all of a sudden changed into this. I mean, why is it giving Group1 and Group2 names?
If I try
>resultsNames(dds_RNA, name = "Group_NACTT_vs_NACCC") Error in resultsNames(dds_RNA, name = "Group_NACTT_vs_NACCC") : unused argument (name = "Group_NACTT_vs_NACCC")
Similary, using a contrast results in errors as welll? I am very confused as it has always been working. Help would be appreciated!