I'm using deseq2 for a RNAseq experiment with 2 genotypes and 5 conditions (2 replicates for each combination of genotype and condition). When I use the deseq command to perform a comparison, I get different results if all experiments are in the DESeqDataSet than when only the 2 compared experiments are in the DESeqDataSet, what is expected as the estimation steps for the model parameters look at all the samples in the DESeqDataSet. Then, if I try to apply lfcShrink with the DESeqDataSet with all experiments, it takes forever. I've waited for 24 hours and still no results. As I have many comparisons, this is not an option. Same thing with rlog. Is it normal? How should I proceed?