[BioC] difference between Affy & spotted arrays

[w.huber at dkfz-heidelberg.de]

Hi,

> 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.

Even for spotted arrays, if the amount of DNA deposited on the array by
the print-tip is well in excess of the reverse-transcribed DNA that is
going to hybridize against it, the exact array-to-array variations of the
deposited amount may not necessarily matter so much for the total measured
fluorescence signal. This should be a valid assumption for low-expressed
genes.

Best regards

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/mga/whuber
-------------------------------------


On Mon, 28 Jul 2003, Naomi Altman wrote:

>
> 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
>
>