If you have the DBMS_STATS package available on your version of Oracle then you should be using that. It is faster (it can be parallellized) and in some cases more accurate.

Other than that, if you make sure always to specify one or more of the following FOR clauses then you will always be sure what is going on ...

... for table
... for all indexes
... for all indexed columns

eg. analyze table my_table compute statistics for table for all indexed columns for all indexes;

see SQL reference for complete syntax.