[BioC] processCGH in snapCGH package

[jhs1jjm at leeds.ac.uk]

Hi John,

Unfortunately that was a typo and hasn't fixed the problem but thanks for
looking.

Regards

John

Quoting "J-C. Marioni" <jcm68 at hermes.cam.ac.uk> on Wed 26 Sep 2007 16:59:34 BST:

> Hi John,
>
> Having a quick look through your code, I think that the line
> RG2$design <- c(-1-1)
> is incorrect.
>
> It should be
> RG2$design <- c(-1,-1)
> I think.
>
> Hope this helps!
>
> Cheers,
> John
>
> On Wed, 26 Sep 2007, jhs1jjm at leeds.ac.uk wrote:
>
> > 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
> >
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