advice on methods for comparison

[Kotoro]

I am trying to compare quality of paraffin embedded samples against frozen samples. (Cancer tissue samples and normal tissue samples from human tumors). I would assume one of the things to do would be a comparison of expression given by sequencing runs on both samples. What are the best tools/methods to use for this comparison and are there any other experimental methods or data that I should be using as well?

I have been trying to learn how to use cufflinks but I'm not so sure cufflinks is the right way to go for this. (Even if it is, what to do with the output to get a useful answer as to whether the samples are good quality becomes another question entirely).

So, I am in need of some good direction and advice.

[Kotoro]

I'm guessing the delay in response is due to this not being a very simple answer. (I had thought so.)

Still slogging through the data, trying to think of way to effectively compare the sequencing runs (and th samples themselves, regardless of sequencing.)