I have 4 different groups (species) that I want to look into their differential gene expression. I call them A, B, C and D.
I have 5 - 8 replicates for each group and I am using DESEQ2 for the analysis.
I am facing a difficulty which I cannot interpret.
I first made a separate data frame for each pairwise comparison, that is A vs B, A vs C, etc. I then created a dds data matrix for each pairwise comparison and then called the
DESeq function. Using
results, I obtained the number of significantly differentially expressed genes.
I then learnt about the
contrast option. So, I made the dds data matrix this time using all groups A, B, C and D and proceeded with the
DESeq function. I then used
results function with
contrast to get the output of each pairwise comparison, A vs B, A vs C, etc.
I get different number of differentially expressed genes in the two comparisons. Why is that the case?
PS: I have posted this question to the bioconductor forum: https://support.bioconductor.org/p/131229/#131235