[BioC] processCGH in snapCGH package

[jhs1jjm at leeds.ac.uk]

Quoting Sean Davis <sdavis2 at mail.nih.gov> on Wed 26 Sep 2007 17:30:18 BST:

> 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.
>
> You can't quote variable names like above.  I'm not sure that is going
> to fix the problem, but until the syntax is correct, it will be hard to
> diagnose the issue.
>
> > 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.
>
> I would use the LogRatio column of the Agilent file without any further
> normalization.  The LogRatio is already background corrected.  The CGH
> algorithms in snapCGH do not depend on the center of the data, so there
> isn't really a need to do any further median centering, etc.  In fact,
> there are probably better methods to center the data, but these use the
> segmented data.
>
> Hope that helps.
>
> Sean
>
Hi Sean,

I'm struggling to import the LogRatio column from the Agilent text files. I'm
using read.delim2 but this is bringing my machine to a standstill and after 45
mins hadn't finished. Is the following the same:

> RG1 <- read.maimages(targets$File_names,source="agilent")
> RG2 <- readPositionalInfo(RG1,"agilent")
> RG2$design <- c(1,-1)
> RG3 <- backgroundCorrect(RG2,method="none")
> MA1 <- normalizeWithinArrays (RG3,method="none")
> LogRatio <- MA1$M

Having just looked at the text file it doesn't appear to be. I've looked through
the data import R guide but haven't found anything yet.

Thanks again
John