[BioC] two color array vs. one color array

Naomi Altman naomi at stat.psu.edu
Wed Dec 17 13:53:21 CET 2008

Dear Leon,
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.


>Hi Naomi,
>Naomi Altman wrote:
>>Yes.  Performance difference relative to what?  Reference design? 
>>Loop design?  Affy array?
>Thanks for your answer. I am new to array analysis, and don't have a 
>clear concept of performance. Suppose I have 2 samples to be 
>compared, should I choose one 2-color array or 2 one-color arrays? 
>Which one is better? If the results are similar, one 2-color array 
>will be more cost-effective.
>Besides, if a two-color array can be used as 2 one-color arrays, why 
>do people still use one-color array widely? Maybe my question is very naive .
>Thanks again.
>>At 06:17 AM 12/16/2008, Leon Yee wrote:
>>>Hi all,
>>>    The question is not related to some specific bioconductor package,
>>>but it is a question about array data analysis: Could a two-color-array
>>>be used as two one-color-array?
>>>    For example, I have 2 two-color-arrays, one is sample1/sample2, the
>>>other is sample3/sample4. Could I treat them as 4 one-color-arrays with
>>>sample1,2,3,4? If yes, what is the performance difference?
>>>    Thanks.

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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