DNA microarray analysis allows you to compare different populations of RNA transcripts.
For example, you might want to compare the transcription levels of gene x in muscle cells versus blood cells, but imagine being able to ask the same question for every gene in the human genome - ie. how do the transcript levels of all the human genes compare in muscle cells versus blood cells. This type of analysis has been enlightening in terms of teaching us exactly what makes a muscle cell versus a blood cell, but it has been particularly powerful as a research tool for cancer biology where it is not as easy to tell apart a normal versus a cancerous cell - especially in the early stages.
The Genetic Science Learning Center at the University of Utah has put together a virtual DNA microarray lab to allow you to try this technique out.