Thresholding the data to 1 is convert the values which are less than 1 to 1. This is done because a values less than 1 would give large negative value after log transformation.
 Now, any entity with the value 1 after log transformation would give a value of 0 in GeneSpring. However, when we threshold the value to 0, it would not give any value after log tranformation and hence empty boxes would be observed.
So, if would like to filter entities with missing value , you could threshold to 0 and then, go to Utilities and select “Remove entities with missing value”.