[BioC] Agilent CGH data

[jhs1jjm at leeds.ac.uk]

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.

Regards

John