Hi!
Could you please also provide additional information, such as sequencing run of your datasets?
Dada2 process all data sample by sample, so in my understanding the number of samples should not affect each sample output.
But here, it is indicated, that one should process different runs/lanes separately, since running samples from different sequencing runs may affect quality filtering step in Dada2.
UPD from @jwdebelius
Adding more samples, even from the same run, also may slightly affect the output for all samples, since
Dada2 analyzes the per run error and then fits a model based on the available data