[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.
HTH,
Jim
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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
More information about the Bioconductor
mailing list