Efficiency: whole vector and for loop methods

Dear R-help,

As a generalization, is it more efficient to use a single method to 
selectively transform items in a matrix?  Preferably whole-vector, yes; but 
if one of the column vectors compels the use of a "for loop", is it then 
faster to do all of the transformations for the matrix via that "for loop", 
rather than use a mixture of methods on a column-wise basis?

TIA

graham lawrence