[BioC] creating a copy number array data object in DNA copy

James W. MacDonald jmacdon at med.umich.edu
Mon Sep 10 21:36:09 CEST 2007

Hi John,

jhs1jjm at leeds.ac.uk wrote:
> Hi, I'm using R 2.5.0 on openSUSE 10.2 x86_64. I'm using some agilent CGH data
> and thought the DNA copy package could be of some use. I'm trying to create the
> copy number array object using the CNA function.
> Usage:
>   CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"),
>                  sampleid=NULL)
> I've currently got the normalized data, xls file written using write.marray from
> the marray package. I've saved this as a csv file in the working directory and
> read it ito R using read.csv. This seems to have worked.
> data <- read.csv("maLoessNormResults.csv")

Using 'data' as a variable name isn't a really good idea, as you are 
masking an existing function of the same name.

> Not to sure where to go from here as i'm unsure about the genomdat argument.
> Will the read.csv function create a data frame? I was under the impression by
> typing data$ProbeName would bring me up all the values from the ProbeName
> header in the csv file but R returns NULL. Sorry if this is somewhat basic but
> any help/point in the right direction is much appreciated.

I would normally point you towards the help for CNA(), but it appears 
you have already found it. However, did you read the next section after 

I get


genomdat: a vector or matrix of data from array-CGH, ROMA, or other
           copy number experiments. If it is a matrix the rows
           correspond to the markers and the columns to the samples.

so you definitely don't want a data.frame (which the help page for 
read.csv says you will end up with):


      A data frame ('data.frame') containing a representation of the
      data in the file.

In addition, it appears you only want genomdat to contain CGH data 
rather than probe names, etc.

I'm not sure what you should get from data$ProbeName. I assume this 
really was a column name in the csv file in which case it should return 
something other than NULL. In any case, you can always get the column 
names of your data.frame using the names() function.



> Regards
> John
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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