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. Regards, Leon

Yes. Performance difference relative to what? Reference design? Loop design? Affy array? --Naomi 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. > >Regards, >Leon > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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

> 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. --Naomi >Hi Naomi, > >Naomi Altman wrote: >>Yes. Performance difference relative to what? Reference design? >>Loop design? Affy array? >>--Naomi > >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. > >Regards, >Leon > > > >>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. >>> >>>Regards, >>>Leon > > 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