creating a copy number array data object in DNA copy
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@jhs1jjmleedsacuk-2338
Last seen 8.4 years ago
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") 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$ProbeName would bring me up all the values from the ProbeName header in the csv file but R returns NULL. Sorry if this is somewhat basic but any help/point in the right direction is much appreciated. Regards John GO marray GO marray • 824 views ADD COMMENT 0 Entering edit mode @james-w-macdonald-5106 Last seen 40 minutes ago United States Hi John, jhs1jjm at leeds.ac.uk wrote: > Hi, I'm using R 2.5.0 on openSUSE 10.2 x86_64. I'm using some agilent CGH data > and thought the DNA copy package could be of some use. I'm trying to create the > copy number array object using the CNA function. > > Usage: > > CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"), > sampleid=NULL) > > I've currently got the normalized data, xls file written using write.marray from > the marray package. I've saved this as a csv file in the working directory and > read it ito R using read.csv. This seems to have worked. > > data <- read.csv("maLoessNormResults.csv") Using 'data' as a variable name isn't a really good idea, as you are masking an existing function of the same name. > > Not to sure where to go from here as i'm unsure about the genomdat argument. > Will the read.csv function create a data frame? I was under the impression by > typing data$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 Usage:? I get Arguments: 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): Value: 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. Best, Jim > > Regards > > John > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623