[BioC] CGHcall error

[Daniel Rico Rodriguez]

Hi James,

Check the new vignette from the latest BioConductor version: now you  
must create and work with CGHcall objects, as the new version does not  
support data.frames directly (but there is a function that takes the  
data.frame with raw data and converts it to the corresponding CGHcall  
package).

Daniel




On Oct 3, 2008, at 3:45 PM, James Morris wrote:

> Hello,
>
>
>
> I have been using CGHcall to analyse our aCGH experiments for the  
> past 6
> months and it has been working great (mac os x 10.4, R 2.7.0)
>
>
>
> However we recently got a new server (mac os x 10.5) and on to it I
> installed the latest version of R 2.7.2 and CGHcall, but now CGHcall  
> no
> longer works!
>
>
>
> It gives the following error:
>
>
>
> Skipping normalization ...
>
> Smoothing outliers ...
>
> Error in function (classes, fdef, mtable) :
>
>  Unable to find an inherited method for function "copynumber", for
> signature "data.frame"
>
> Calls: normalize ... inherits -> <Anonymous> -> copynumber ->  
> <Anonymous>
>
> Execution halted
>
>
>
> Any help would be great
>
>
>
> Thank you,
>
>
>
> James Morris
>
>
>
> Gynaecological Cancer Research Laboratories,
>
> UCL EGA Institute for Women's Health,
>
> University College London,
>
> Paul O'Gorman Building,
>
> 72 Huntley Street,
>
> London WC1E 6DD
>
> United Kingdom
>
>
>
> Telephone: 020 3108 2002
>
>
> 	[[alternative HTML version deleted]]
>
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********************************************

Daniel Rico Rodriguez, PhD.
Structural Computational Biology Group
& Bioinformatics Unit
Spanish National Cancer Research Center, CNIO
Melchor Fernandez Almagro, 3.
28029 Madrid, Spain.
Phone: +34 91 224 69 00 #3062
drico at cnio.es
http://www.cnio.es

********************************************




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