[BioC] two color array vs. one color array

[Leon Yee]

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