Hi, 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? thanks simon

> >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? phenoData is a S4 class defined in the Biobase package. Type ?phenoData (after loading Biobase) for the descriptions and examples of creating a phenoData. > >thanks >simon > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

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) HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Simon Kidd <kidd@mail.rockefeller.edu> 04/08/04 02:16PM >>> Hi, 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? thanks simon _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

At 2.36pm -0400 8/4/04, James MacDonald wrote: >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) > >HTH, > >Jim Thanks. On my system the widget has no scroll bars which means when entering the covariance that I cannot enter all 44 CEL files. Is the lack of scroll bars a feature or a problem with my setup? Iam using R1.9 beta and OSX10.3. thanks, Simon