[BioC] Question about Microarray before/after treatment, Paired Analysis

[Haiyan Wu]

Look for reference about paired analysis about microarray.

I have a data set about a microarray experiment for same patients before and
after treatment. Data Layout is show in belwo
Table 1
	Patient 1 Before surgery	Patient 1 after surgery	Patient 2
Before surgery	Patient 2 after surgery	..	
Gene 1						
Gene 2						
.						
.						

The question of interest is to compare results before and after treatment
and thus identify genes of interest, classify patients, and identify
patients who respond to the surgery. Also, the sample size needed for
further experiment is of interest. Typical statistical method would be
paired t test. But I don't know how to take account the correlation between
genes and how to adjust for the false discovery rate.

I looked at some references. But they're either about independent sample
groups or about complex time series using Markov Chains or Bayesian. Is
there any reference for this type of experiment? Does Bioconductor have a
package for this type of analysis?

I'm familiar with statistical method and bioconductor software. But I'm
still new to microarray analysis. Any reply is sincerely appreciated. 

Haiyan 

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