[BioC] read.phenoData

Martin Morgan mtmorgan at fhcrc.org
Thu Jun 14 17:08:14 CEST 2007

>From the man pages, read.phenoData uses read.table. read.table has
arguments header=FALSE, and row.names to influence row names. Provide
approrpiate arguments to read.phenoData, and they ware passed to

varLabels _describes_ (i.e., is metadata about) the variable (column)

Looking forward two steps. In the released version of Biobase
read.AnnotatedDataFrame is a replacement for read.phenoData,
appropriate for creating an ExpressionSet. In the devel version of
Biobase, read.AnnotatedDataFrame has been changed to include the
metadata about columns in the file to be parsed.


Seth Falcon <sfalcon at fhcrc.org> writes:

> carol white <wht_crl at yahoo.com> writes:
>> hi, What is the use of having samples name in the first column and
>> variable names in the first row of a phenoData file if sampleNames is
>> not instanciated to the sample names nor varLabels to the value of
>> variable names? having 4 variables and 3 samples for ex, there will be
>> 5 variables and 4 samples in the phenodata object. How can I modify to
>> the object to an object of 4 var and 3 samples with samples and
>> variable names?
> I'm having a hard time parsing your email message.  I wonder if you
> could give some concrete code examples of what you are trying to do...
> + seth
> -- 
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> http://bioconductor.org
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Martin Morgan
Bioconductor / Computational Biology

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