I'm a student of biology working on finishing off my thesis but severely lack an understanding of statistical analysis. Can any of you point me in the right direction?

Basically I want to compare the culture results of 3 different types of culture media and 3 different treatments, which were tested using the same samples, approximately 48 samples. Wanted to compare their positive rates (pos or neg), and later on their concentrations. At the end I wanted to be able to conclude whether a specific type of media had a significantly higher positive rate and whether a given type also had a significantly higher final concentration.

But alas my understanding of statistical analysis is minimal to non-existent. So far I figure I'll end up using on or more of these: the exact test of goodness-of-fit (exact binomial test), Fisher's exact test, paired t-test, student t-test or the Wilcoxon signed-rank test.

Got them low sample sizes, and probably an uneven distribution. Theoretically I could transform the data but that seems like adding oil to my raging brain fire.

So yeah any statistical wizards around?