[BioC] processCGH in snapCGH package

[jhs1jjm at leeds.ac.uk]

R 2.5.0 on openSUSE 10.2 x86_64.
Hi,

I'm using the snapCGH package to analyse 2* 244k agilent CGH arrays with the aim
of identifying regions of gain/loss.
So far i've done the following:

>targets <- readTargets ("targets.txt")
>RG1 <-read.maimages (targets$File_names, source="agilent")
>RG2 <- readPositionalInfo (RG1,source="agilent")
>RG2$design <- c(-1-1)
>RG3 <- backgroundCorrect (RG2,method="minimum")
>MA1 <- normalizeWithinArrays (RG2,method="median")

then
> MA2 <- processCGH(MA1,method.of.averaging=mean,ID="MA1$genes$ProbeName")
Error in order(na.last, decreasing, ...) :
        argument 2 is not a vector

I've looked at ?processCGH and am following the vignette for the snapCGH package
fairly closely. Can anyone help with the error.

Also i'm unsure of what background correction to use and normalization function
(I've been informed that non-linear methods are unsuitable). Also if anyone has
any experience of Agilent CGH arrays could they also tell me whether the
default estimates used for the foreground and background intensities in
read.maimages are suitable. I'd like to determine the most suitable methods
before as I think the segmentation may take some time on my machine. If its a
case of trial and error then then thats fine. Thanks for any input.

Regards

John