[BioC] two color array vs. one color array

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Dec 17 16:21:07 CET 2008


On Dec 17, 2008, at 8:18 AM, Leon Yee wrote:

> Hi Naomi,
>> People generally use what is most cost effective for the  
>> application.  Some 1-color systems are more accurate than some 2  
>> color systems.  And some 1-color systems are cheaper per sample,  
>> processed.  Some investigators are interested in particular genes  
>> which may be printed on some commercial arrays but not others.   
>> (Most "whole genome" arrays do not cover the whole genome.)   
>> Experimental design is more picky for 2 color arrays because the  
>> within array variance is usually smaller than the between array  
>> variance... If you are using commercial arrays, you also need to  
>> consider the bioinformatics tools available.
> Thank you very much! I'm now much more clear about this.

These papers might be useful for you regarding the use of different  

The MicroArray Quality Control (MAQC) project shows inter- and  
intraplatform reproducibility of gene expression measurements

The "Related Articles" listed at this page have some interesting  
looking follow up papers, for instance:
Performance comparison of one-color and two-color platforms within the  
MicroArray Quality Control (MAQC) project.

Also, a recent paper Genome Research addresses array platform issues  
that are specific to their use in ChIP-chip experiments:

Systematic evaluation of variability in ChIP-chip experiments using  
predefined DNA targets

Hope that helps,

Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University


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