[BioC] Agilent control probes

[Sean Davis]

On Sat, Apr 19, 2008 at 12:46 AM, Kasper Daniel Hansen
<khansen at stat.berkeley.edu> wrote:
> We are constructing a microarray and we (I) want some normalization
>  controls on the array. We are testing the Agilent platform and they
>  seem to have a standard control mix + probes you can purchase for a
>  set prize. It seems to be viral or bacterial genes covering a wide
>  range of concentrations.
>
>  Is anyone familiar with using these probes for normalization? I am
>  wondering whether the number of probes is great enough (well, I am
>  actually wondering how many probes you get for each transcript).
>  Should we consider making our own mix (which we might do anyway test
>  the difference). Any comments on or off-list would be appreciated. We
>  are going to do a potential huge number of arrays, so I want to get
>  this as good as we can.

Hi, Daniel.  Using spike-in controls for normalization is not going to
be ideal, I don't think.

Is this a CGH array, tiling array (expression, CGH, chIP-chip),
expression (two-color, one color)?  The array type will dictate to a
large extent what types of probes you need to include for
normalization and controls.  In some cases, you may not need to
include anything special.

Sean