[BioC] Clustering question

[Srinivas Iyyer]

Dear group, 
apologies this question is not directed to any
bioconductor package, but a simple bioinformatics
question. 

I have gene expression data cDNA array. 

The design is:
total 6 samples (3 treated, 3 untreated) with time
points. 

Time 1:  Sample1-treated/Sample1-untreated
Time 2: Sample 2- treated / Sample 2-untreated
Time 3 : Sample 3 - treated / Sample - 3 untreated

Now I have fold-changes for Time1, Time2 and Time3. 

Is it possible to do a clustering here by creating a
matrix:

Genes   Time-1   Time-2  Time-3
G1
G2
..

Is doing a simple Hierarchical clustering between all
time points a meaningful approach because the fold
changes are specific to a particular time point. 
(reference samples is not universal but specific to a
timepoint). 

Could anyone kindly educate me here. Apologies again
if this question is a misfit. 

Thanks
Srini


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