[BioC] statistical test help -RT-PCR data?

[John Alexander]

Hi all,
I'll try list my problem in the following below.
Data: from RT-PCR experiment (log(2^-delta delta t) data)
Experiment: (A1,A2,A3,B1,B2.B3) samples belonging to 2 groups (A,B) and want to find the differential expressed genes 
Statistical test : t-test or use limma between 2 groups. It works fine.
Software : R [Packages: genefilter,limma]

Problem: We know that A3 is slightly different from the rest of the samples by viewing the boxplot so I want to find the differentially expressed genes of A3 against the group B (B1,B2 and B3)….This means 1 sample against a group of 3. As it is I don't have enough samples and using a t-test using sample A3 and mean of (B1,B2,B3) seems statistically incorrect for this purpose, I tried using LIMMA package thinking it should produce sensible results. Would this be correct or should I be using any other tests. 
Any help rendered is appreciated.
cheers,
John.