[BioC] two color array vs. one color array

[Steve Lianoglou]

Hi,

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  
microarrays:

The MicroArray Quality Control (MAQC) project shows inter- and  
intraplatform reproducibility of gene expression measurements
http://www.ncbi.nlm.nih.gov/pubmed/16964229

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.
http://www.ncbi.nlm.nih.gov/pubmed/16964228

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
http://genome.cshlp.org/content/18/3/393

Hope that helps,
-steve

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

http://cbio.mskcc.org/~lianos