[BioC] difference between Affy & spotted arrays

[Jenny Drnevich]

>
>I am not that familiar with Affy, but I think that, because their setup is
>very different (e.g., multiple probes per clone), the direct analogy "if we
>do it with Affy we ought to be able to do it with cDNA" does not really hold
>just like that.

I had also been wondering about this issue of why spotted chips must be 
referenced but Affy chips are not. I got a seemingly logical explanation 
from Jeff Townsend: Array to array variation per spot in the amount 
deposited, shape of the spot, etc., is extremely high for spotted arrays, 
even with the best spotters and protocols, therefore you always need 
expression levels to be referenced. Affy's photolithographic method is 
*supposed* to have much greater precision in the number & placement of 
probes per feature, making direct array to array comparisons possible.



Jenny Drnevich, Ph.D.
Department of Animal Biology
515 Morrill Hall
505 S Goodwin Ave
Urbana, IL 61801
USA

ph: 217-244-6826
fax: 217-244-4565
e-mail: drnevich at uiuc.edu