[BioC] processCGH in snapCGH package

[jhs1jjm at leeds.ac.uk]

Quoting jhs1jjm at leeds.ac.uk on Wed 26 Sep 2007 22:54:01 BST:

> 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
>
Additionally Sean I tried:

>LogRatio <-log2(RG1$R)-log2(RG1$G)

This gives me different results to the text file?
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