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12-15-2011, 07:40 PM   #21
Godevil
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Location: Japan

Join Date: Feb 2011
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Quote:
 Originally Posted by Dbarker06 Why not just arrange the 1680 plates into a 40X42 array. Then make pools of all the samples in each row of 40 and each column of 42. PCR these 82 pools. The results give you the row and column position of each positive 96 well plate in your 40x42 array. Then test each clone in the positive plates. You won't miss any positives--if there happen to be two positives in the same plate you will find that. Assuming that there are three positives,you will do less than 400 PCR reactions to find the individual positive clones.

What you said is the 2 dimension-based design. But I prefer to use 3 or higher dimension, which can save me much more time and money for PCR. I've already considered lots of screening design. Higher dimention means more false possitive.

As in the 2-dimension method, the most false positive results is 3^2-3; in 3D is 3^3-3. The only way to reduce the false positive is to make sure only one positive clone locates in one superpool.

Last edited by Godevil; 12-15-2011 at 09:26 PM.

12-15-2011, 07:43 PM   #22
Godevil
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Location: Japan

Join Date: Feb 2011
Posts: 22

Quote:
 Originally Posted by ECO For what it's worth, I'm really glad this wasn't homework and actual experimental biology. In the future (and anyone reading this contemplating doing the same bounty for help...)...please be honest. As Simon said, the fun is in the biology...you're much more likely to get help being honest (with or without a bounty).
Hey, I just want to make my question simple to be understand for everyone. It has nothing to do with honest or not.

Last edited by Godevil; 12-15-2011 at 07:46 PM.

 12-16-2011, 06:01 AM #23 HESmith Senior Member   Location: Bethesda MD Join Date: Oct 2009 Posts: 503 The recommended two-dimension design, followed by screening individual candidate plates (using 8x12 matrix, if you want to minimize the number of PCRs) is the most efficient method. If you're committed to higher order screening with fewer false positives, you may be able to incorporate a Steiner triple system (see http://www.nature.com/nmeth/journal/...nmeth1063.html for a similar application).

 Tags experimental design, probability