Matched pair analysis for small sample size

Question

[manali.rupji]

Hello All,

I have a data set for analysis provided to me. It includes 3 matched paired samples i.e. Diagnostic vs Recurrent. Also provided to me are a set of genes (group A = 30 genes) and a set of genes (not A = 2000 genes) based on some previous analysis on another sample set. I was told that there is a biological relevance to use this gene set A for the downstream analysis.

H0: (R-D)notA = (R-D)A
Ha: (R-D)notA > (R-D)A

It is of interest to retain the matching.

Given such a small size, I could perform permutations (but will have to un-match the samples to get at-least a few permutations). Could some one suggest any alternate ways to analyze this data?

Any help in this regard would be very valuable.

Thanks in advance,

Regards, M