I performed variance stabilized transformation on raw gene counts. Now for the future purpose, I want to combine replicates and calculate the log fold change values between control and experimental condition (I don't want to perform differential expression analysis). How can I combine the VST counts? I tried combining them by mean() which is basically geometric mean as the values are in log. But I noticed that log fold change distribution is drastically shifted (from zero) for some experimental conditions with lot of replicates (more than 2). Any suggestions?