I believe I am using the DESEQ2 Formula correct but after getting some unexpected results I would like to double check with you:
I want to check the effect of Vitamin D on patients and I have a group who takes Vitamin D and a group who doesn't take Vitamin D. Since these groups are quite different I need to adjust for Gender, Age, Batch and BMI.
My formula is:
dds <- DESeqDataSetFromMatrix(countData = cts, colData = colData, design ~ batch + Gender + Age + BMI + Vitamin_D_Group
I understand that I need to put the factor I want to analyse at the end and the other variables I am adjusting for in the beginning of the formula, following this "With no additional arguments to results, the log2 fold change and Wald test p value will be for the last variable in the design formula, and if this is a factor, the comparison will be the last level of this variable over the reference level".
Can anyone confirm me that this is correct?
Thank you so much, Bine