[BioC] Clustering non-biological replicate chips

[Naomi Altman]

I agree with your approach.

--Naomi

At 05:47 PM 4/13/2005, Ken Termiso wrote:
>Hi all,
>
>I have an experiment with several control and several experimental 
>replicate chips, and the chips are not actual biological replicates, but 
>rather represent replicate hybridizations or amplifications. In terms of 
>the data to be input into a clustering algorithm such as kmeans, would it 
>be better for me to calculate a single average value for the control side 
>and one for the experimental side than it would be to input all of the 
>replicate chip data? It seems that using all of the replicate data points 
>from non-biological replicates would only help partition non-biological 
>aspects of the data and not help answer questions regarding what is 
>happening biologically between the control and experimental cases.
>
>Thanks in advance,
>Ken
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111