[BioC] CGH microarrays significance test

[Sean Davis]

On Wednesday 21 March 2007 12:06, Ramon Diaz-Uriarte wrote:
> Dear Joao,
>
> On Wednesday 21 March 2007 16:33, João Fadista wrote:
> > Dear list,
> >
> > I have a CGH microarray experiment where I compare male vs. female in
> > each sample (3 technical replicates with dye swaps = 6 samples). So in
> > theory I would expect to see a difference in log2ratios of the X
> > chromosome compared to the autosomes. This experiment is made mainly to
> > assess/optimize the reliability of the protocol and the in-house
> > microarray platform for CGH microarrays experiments.

A very useful measure for CGH when comparing protocols, etc., is a measure of 
signal divided by a measure of noise (signal-to-noise ratio).  You could use 
a very simple measure like the mean or median of the X chromosome minus the 
mean/median of the autosomes as the signal and then the sd or MAD of the 
autosomes as the noise.  Each array can then be summarized by a single 
number.  Coming up with a statistical test is quite interesting, but I don't 
think it is necessary for what you are describing.  

As with all microarray analyses, there is no substitute for visualizing the 
data, doing adequate preprocessing (you can't just loess-normalize the arrays 
as you would with expression arrays), and generating quality-control plots.

Sean