[BioC] processCGH in snapCGH package

[J-C. Marioni]

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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