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Question: exprSet
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gravatar for Jiuzhou song
12.1 years ago by
Jiuzhou song100
Jiuzhou song100 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? 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
ADD COMMENTlink modified 12.1 years ago by James W. MacDonald43k • written 12.1 years ago by Jiuzhou song100
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gravatar for James W. MacDonald
12.1 years ago by
United States
James W. MacDonald43k wrote:
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@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.
ADD COMMENTlink written 12.1 years ago by James W. MacDonald43k
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