[BioC] exprSet

James W. MacDonald jmacdon at med.umich.edu
Sun Apr 17 14:26:49 CEST 2005

Jiuzhou song wrote:
> Dear Dr.Robert:
> Thanks your prompt response.
> Yes, I looked at the vignette in Biobase, and followed the procedure.  
> It is not clear, what are originally formats of the  geneCov and  
> geneData? 

You can always determine this for yourself.

 > data(geneCov)
 > mode(geneCov)
[1] "list"
 > is.data.frame(geneCov)
[1] TRUE

Note that a data.frame() *is* a list.

So geneCov is a data.frame, which you already know is the result of 
read.table(), so you can either read in a text file using read.table, or 
you can make one from within R. See ?data.frame

 > data(geneData)
 > mode(geneData)
[1] "numeric"
 > is.matrix(geneData)
[1] TRUE

So geneData is a matrix. As Robert already pointed out, you cannot use a 
data.frame() for the exprs slot of an exprSet. However, it is simple to 
convert a data.frame() to a matrix, using as.matrix(). You can either 
read in your data using read.table() and then convert to a matrix, or 
you can read the data into a matrix directly using scan(). However, it 
is simpler to use read.table().

Now, you can follow the code in the vignette to instanciate your exprSet.



I also traced the libary of the geneCov and GeneDatar, the
> geneCov is phenotype data, and geneData is gene  expression data. They 
> are wraped by R, not original one. The data  statement only load data 
> with R format. I am sure with a way can build a format like geneCov or 
> GeneData, I don't know how to do it from originally gene expression data 
> and phenotype data.
> In addition, I understand the read.table not to creat a matrix, only a  
> data.frame, how can I creat a matrix directly from raw data? Thanks  again.
> Yours
> John
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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