I am having trouble to decide what statistical test to use on my data because I have one factor grouped within another. Here is my experimental design: I have two cell lines, one infected with a bacteria (I) and one uninfected (U). I have split each of theses cell lines into two groups and treated one group with a chemical treatment (T) and one with a control treatment (C). So I have four groups of cells:

Infected-Treated

Infected-Control

Uninfected-Treated

Uninfected-Control

The uninfected cell line is like a control for the infected cell line.

I then ran a gene expression microarray with technical triplicates, so my dependent variable is continuous and normally distributed. First I need to compare T vs. C

*within*each cell type (U and I)to determine the affect of the treatment on that cell type (can i use a unpaired T.Test for this?). Then ultimately I would like to compare the affect of the treatment

*between*infected and uninfected cell types to determine how the bacterial infection alters genes response to the chemical treatment. Which statistical tests would be appropriate for this experimental design?

Any help for this thread would be greatly appreaciated!

Many Thanks