[BioC] Agilent CGH data

[Sean Davis]

jhs1jjm at leeds.ac.uk wrote:
> R 2.5.0 on openSUSE 10.2 x86_64.
> 
> Hi,
> 
> I'm using the arrayQuality package to analyse 3 44k Agilent CGH arrays with the
> aim of identifying regions of gain/loss.
> 
> With the HTML report generated using the agQuality function i'm not getting the
> coloured loess curve on the MA plot for raw M. Additionally i'm only getting 1
> value for the dot plot of controls normalized M values (-)3xLv1 (n=330) and
> likewise for the control A values. Alternatively when I run the maQualityPlots
> function on my mraw object created in marray  I get these but don't get the
> comparative box plot.
> 
> Firstly is this important as I'm unsure of how useful the comparative boxplots
> are as some values are NA? Secondly is this an appropriate tool to use and are
> there any others that may be of more use both for quality control and for
> analysis further down the line? Thankyou kindly for any input.

Hi, John.  Are these CGH arrays or expression arrays?  The two probably
need some different treatment.  You imply you are using CGH arrays in
looking for regions of gain/loss.  Is this the case?

Sean