[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
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.
> CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"),
> 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$ProbeName would bring me up all the values from the ProbeName
> header in the csv file but R returns NULL. Sorry if this is somewhat basic but
> any help/point in the right direction is much appreciated.
I would normally point you towards the help for CNA(), but it appears
you have already found it. However, did you read the next section after
genomdat: a vector or matrix of data from array-CGH, ROMA, or other
copy number experiments. If it is a matrix the rows
correspond to the markers and the columns to the samples.
so you definitely don't want a data.frame (which the help page for
read.csv says you will end up with):
A data frame ('data.frame') containing a representation of the
data in the file.
In addition, it appears you only want genomdat to contain CGH data
rather than probe names, etc.
I'm not sure what you should get from data$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.
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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