How to compare the text populated correctly

There are many different ways to do comparisions in TC/TE.  Can you provide any more information about what is happening in the script?  Are you running both applications with the script?  There are far too many variables in solving your problem, so an explaination of what you are actually trying to do would be quite helpful.  In the simplest form, you could store the value from app A as a project variable and then run a comparison in app B.  There is always the use of external *.txt docs as well, if you plan to run them separate from each other.  If they are integrated with a database, you can execute queries from TC/TE.  I can continue to throw guess after guess at your problem, but without further detail, I'm stabbing in the dark.