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What form is the data in currently? Do you have the scanner output files? --Naomi At 05:53 PM 1/22/2007, Sarah Highlander wrote: >I?m just getting started and need to create an exprset. Searched the web and >I can?t find an explanation. I?m working on a Mac OS 10.4 > >Thanks, > >Sarah >Sarah K. Highlander, Ph.D. >Associate Professor >Baylor College of Medicine >Department of Molecular Virology and Microbiology >One Baylor Plaza, MS280 >Houston, TX 77030-3498 > >713-798-6311 Voice >713-798-6802 FAX >sarahh at bcm.tmc.edu > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Hi Sarah, You may find the ExpressionSet tutorial presented at last October's BioC intro course to be useful: http://bioconductor.org/workshops/2006/biocintro_oct/labs/Expression Set/ Have a read through ExpressionSetIntro-solved.pdf. It walks through the details of building an ExpressionSet object from scratch. Naomi Altman <naomi at="" stat.psu.edu=""> writes: > What we do is to to use read.table or read.delim > to read the data into a dataframe. > > I have not found it necessary to create an > exprSet object from the dataframe. Actually, I think there are a lot of advantages to getting your data into an ExpressionSet (that's the new and improved version of exprSet). Here are a few reasons: * Automatic/enforced alignment of pheno data (e.g. clinical vars) and expression data. If your pheno data gets misaligned, your analysis will be compromised. * Easy subsetting of genes (probe sets) and/or samples. Again, once you've aligned the data, you don't have to think about it again. If you have separate data.frame or matrix objects for the expression values and your phenotype description data, you have to do this manually for each subset you want to explore. * Many Bioconductor packages make it easy to apply analysis techniques if what you have in hand is an ExpressionSet. For some examples, browse recent BioC workshops on the website. > However, if you feel it is necessary, you can create each component > using the columns of the dataframe as needed and then set the class > to exprSet. This is a bad idea and is not guaranteed to work. Your next suggestion is much better... > The documentation for an exprSet is in Biobase. (Note the uppercase > S.) It shows how the "new" command can be used to create the > exprSet once you have all the components. (Components can be > empty.) However, exprSet is being replaced by ExpressionSet, so it would be better to start there. Best, + seth

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