[BioC] CGHcall and Normalization

[Salih Tuna]

Hi Martin,
Thanks for your reply. I managed to run the code. AS you said I needed
to adjust the data.
But now the output seems something like this:

normalized.data
cghRaw (storageMode: lockedEnvironment)
assayData: 3552 features, 5 samples 
  element names: copynumber 
phenoData
  sampleNames: AdCA10, SCC27, ..., SCC39  (5 total)
  varLabels and varMetadata description: none
featureData
  featureNames: RP11-465B22, RP4-785P20, ..., CTB-99K24  (3552 total)
  fvarLabels and fvarMetadata description:
    Chromosome: Chromosomal position
    Start: Basepair position start
    End: Basepair position end
experimentData: use 'experimentData(object)'
Annotation:  

This might be a very stupid question but I was expecting to see the
normalized data which is the same dimension as the raw data. I am sure I
can access the normalized data which is the same dimension as the raw
data. But I don't know how. Could you please show me how to do this?

Best,
salih 

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: 11 June 2011 16:24
To: Salih Tuna
Cc: bioconductor at r-project.org
Subject: Re: [BioC] CGHcall and Normalization

On 06/08/2011 08:47 AM, Salih Tuna wrote:
> Hi,
>
> i am trying to use the normalization function from CGHcall library.
>
> The command i use is
>
>
>
> normal.fullData<- normalize(fullData, method = "median", cellularity =
> 1)
>
> and i get the following error message. How can i solve this issue.
>
> Error in function (classes, fdef, mtable)  :
>
>    unable to find an inherited method for function "copynumber", for
> signature "data.frame"

Hi Salih --

If I

   example(CGHcall)

and look at how normalize() is used, the first argument is 'raw.data' 
and it is

 > class(raw.data)
[1] "cghRaw"
attr(,"package")
[1] "CGHbase"

if instead I

 > normalize(data.frame())
Applying median normalization ...
Error in function (classes, fdef, mtable)  :
   unable to find an inherited method for function "copynumber", for 
signature "data.frame"

so perhaps you are trying to use a data.frame instead of an object of 
'cghRaw', i.e., your earlier work flow needs to be adjusted. If you need

more help, it is best to post a reproducible example, starting from 
sample data available in the package.

Hope that helps,

Martin
>
> best,
>
> salih
>
>
>
>


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