[BioC] Agilent control probes
sdavis2 at mail.nih.gov
Sat Apr 19 13:27:04 CEST 2008
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.
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