[BioC] Dye-swap Design

Naomi Altman naomi at stat.psu.edu
Tue Nov 3 14:07:22 CET 2009


1. Biological dye-swaps are fine.

2. It depends on whether there is a strong dye effect.  Given my own 
experience, I think the dye effect observed by Churchill and Kerr, 
which was limited to a couple of probes, was real, but that much of 
the more pervasive effect reported by others can be attributed to 
technical problems with the dyes.  So, carefully handled arrays, with 
dye protectorants, which not have much dye effect.

3. The pooled samples have smaller biological variance than the other 
samples.  If the variance is dominated by technical variance (e.g. in 
an inbred species) your solution is reasonable.  If it is dominated 
by biological variance, then you are artificially reducing the 
variance estimate that is used for your statistical tests.

Regards,
Naomi

At 10:58 AM 11/2/2009, Jason Pear wrote:

>Dear Listers,
>
>
>
>We have a case-control study and would like to use Agilent 4x44K 
>array.  We only have three biological replicates.  My questions are
>
>
>
>1.  Do we need to use technical dye-swap or we can use biological 
>dye-swap (budget issue)?
>
>
>
>2.  How does the un-balanced dye-swap effect the analysis?
>
>
>
>3.  If we use biological dye-swap and balanced dye-swap, since we 
>only have three samples for each condition.  Can we pool samples in 
>order to balance dye-swap?  Here is the design:
>
>
>
>                Array1                      Array2 
>     Array3                   Array4
>
>Red          caseA                       controlB 
>caseC                   pooled control
>
>Green       controlA                     caseB 
>controlC                pooled case
>
>
>
>Many thanks,
>
>
>
>Jason
>
>
>
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>
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111



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