[BioC] difference between Affy & spotted arrays

[Naomi Altman]

The reason that Affy arrays are not supposed to need a reference is that a 
known quantity of probe is placed on the array by fabrication.  This is the 
same on every array.  On spotted arrays, the material is deposited by the 
print tip, and so may vary from array to array.

Nonetheless, it is prudent to use a titration series for your spiking 
controls, to use for calibration.  Alternatively, using a probe-wise 
normalization (see "expresso" in the affy library) should make all of your 
Affy arrays on the same scale.

---Naomi


At 01:57 PM 7/25/2003 -0500, Jenny Drnevich wrote:


>>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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111