[BioC] CGH microarrays significance test

[João Fadista]

Dear Sean and Ramon,

Thanks for your thoughts of what should I do. I will try to digest your ideas.
I got myself now the book "Mixed-effects models in S and S-plus" for helping me modelling my data.
Wish me luck!

Best regards

João Fadista
Ph.d. student


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-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: Wednesday, March 21, 2007 5:40 PM
To: bioconductor at stat.math.ethz.ch
Cc: Ramon Diaz-Uriarte; João Fadista
Subject: Re: [BioC] CGH microarrays significance test

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