[BioC] S/N ratio in microarrays

[Sean Davis]

On 11/10/05 6:18 AM, "narinder.singh at diagenic.com"
<narinder.singh at diagenic.com> wrote:

> Can somebody point to litterature related to S/N ratio in microarray data. In
> spectroscopy the S/N ratio is typically 30000:1. From what I have gathered S/N
> ratio is a big problem in microarray data. Is there any litterature/study with
> corresponding S/N numbers for microarray data for commercially available
> platforms.
> 
> Thanks in advance.

Narinder,

I don't think this is a well-understood property of array technology.  S/N
is at least probe-dependent and like sample-dependent as well (RNA quality,
etc.), not to mention operator dependent, ozone-level dependent, humidity
dependent, protocol dependent, and many others.  Some experimental designs
(particularly with two-color arrays) can GREATLY affect the S/N ratio at the
level of the final analysis (which is what counts).  I'm not giving an
answer directly, because I'm not sure that one exists and if it does, I
think it applies only to a specific set of samples in a specific lab on a
couple of platforms, etc.

Perhaps someone else has reviewed the literature on this subject and can
give you a better answer.

Why do you ask?

Sean