Hello,

I am learning about experimental qRT-PCR design and I found Hellemans et al., 2007 [1] and Rieu and Powers 2009 [2]. So, I made a experimental design for me [3].

However, I am not sure what package I could use to do the analysis afterwards.

Have you any suggestion to me about:

A. My experimental design;

B. What package I could use to do the downstream analysis.

I was learning about EasyqPCR package, but, may be it need IRC (Control) in all run (plate).

1. http://genomebiology.com/2007/8/2/r19

2. http://dx.doi.org/10.1105%2Ftpc.109.066001

3. http://goo.gl/68h1ul

Marcelo Luiz de Laia
Universidade Federal dos Vales do Jequitinhonha e Mucuri
www.ufvjm.edu.br
Brazil

My lab uses the limma package to analysis qRT-PCR data. We convert Ct values to log2-expression by a simple tranformation such as 40.5-Ct (assuming 40 is the upper limit for Ct values). We use cyclic loess normalization with upweights for the house-keeping probes, then proceed much as for a standard limma pipeline.