Hello everyone,

This may be a basic question but I am facing a problem I do not know how to solve...

Let me explain the situation :

I am working with DNA array analysis and I have four groups (let's call them A,B, C and D). Groups A and B are controls for two distinct populations, C and D are samples from two distinct sick populations. All groups contain 5 members.

A and C are linked (ie they both represent the same population, one sick, the other healthy). B and D are linked as well (represent a different population, again one is sick, the other is healthy).

This gives :

A population 1 healthy
C population 1 sick

B population 2 healthy
D population 2 sick

I want to compare gene expression of some targets genes within these two populations and see if what happens in population 1 between healthy and sick is significantly different from what happens for the same gene in population 2.

Is the fold change for gene1 expression between C and A significantly different from the fold change between D and B ?

Of course both population have the same disease.

I can easily calculate (student test) if the fold change between A and C is significant, as well between B and D, but how can I then compare the A/C fold change with the B/D fold change, and take into account the original expression variability of the samples...

Is the "fold change" difference observed between A and C comparison, significantly different from what is observed between B and D, or do the gene behave similarly in both population 1 and 2 when sick compared to healthy controls ?

Any help would be more than welcome....

Fred