If less than 48/96 samples are being processed, is it possible to leave positions empty with the PAXgene Blood RNA MDx Kit?
FAQ ID -2492

In general, batch sizes other than 48/96 are not recommended because the vacuum profile can be affected. During a limited number of test runs with 48 or 96 sample batches, up to 8 samples were water blanks instead of real samples. In these runs minimal effects were observed with respect to yield and purity of the eluates.