I am working with RNA-seq data and using DESeq2 to perform differential expression analysis. My design has a single factor, diagnosis, which is a multi-level factor with six different diagnoses: 'Craniopharyngioma', 'ATRT', 'Ependymoma', 'Glioblastoma', 'Glioma', and 'Medulloblastoma'.
My design is as follows:
dds <- DESeqDataSetFromMatrix(countData = count_data, colData = meta, design = ~ diagnosis)
I am interested in comparing each diagnosis against 'Craniopharyngioma'. To do so, I tried to relevel the 'diagnosis' factor:
dds$diagnosis <- relevel(dds$diagnosis, ref = "Craniopharyngioma")
However, when I run the results() function without specifying any contrast, I get comparisons with 'ATRT' as the base level, as seen in the names of the coefficients from resultsNames(dds):
 "Intercept" "diagnosis_Craniopharyngioma_vs_ATRT"  "diagnosis_Ependymoma_vs_ATRT" "diagnosis_Glioblastoma_vs_ATRT"  "diagnosis_Glioma_vs_ATRT" "diagnosis_Medulloblastoma_vs_ATRT" How can I interpret this result? Does DESeq2 use the relevelled factor in its calculations, but then print the results with the old base level? I would appreciate if someone could clarify this for me. Thanks, Amdom