[BioC] phenoData

James MacDonald jmacdon at med.umich.edu
Thu Apr 8 20:36:37 CEST 2004

If you look in the Biobase vignette, there is a section that explains
how to make a phenoData object by hand. Basically what you need is a
data.frame containing the phenodata information, and a list
corresponding to the labels you want for the phenoData object.

Alternatively, you can use widgets to make the phenoData object as part
of reading in your cel files.

dat <- ReadAffy(widget=TRUE)



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Simon Kidd <kidd at mail.rockefeller.edu> 04/08/04 02:16PM >>>

I have a beginners  type question. I see that in simpleaffy one tells 
bioconductor what the samples represent through having a  tab 
deliminated covdesc file in the same folder as the .cel files. Other 
packages use phenoData which I gather is seen with the pData(eset) 
command, how does one  make a  phenoData file and where is it kept?


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