[BioC] gene expression baseline adjustment for pre/post treatment

[Jun Xu]

Hi, All,

We have an experiment in which 30 subjects were divided into two groups (15
treatment and 15 control). Gene expressions were measured before and after
treatment for both groups. I am wondering what is the best way to do baseline
adjustment? Several ways of analysis are in consideration.

1. Post treatment gene expression only.

2. Difference in Post/pre treatment

3. ANCOVA using baseline gene expression as covariate for each gene.

Any suggestion? If using ANCOVA, is it required to use the parallel line model?

Thanks

Jun