Thanks Tiago for your email. Please in the future post your questions to the Bioc mailing list (linked from http://bioconductor.org) so that other may benefit. I've cc'd that group, and hope that you do not mind. readExpressionSet requires the name of a file that contains the 'phenoData', i.e., sample descriptions. See the description of this file by consulting the help file for readExpressionSet: > library(Biobase) > ?readExpressionSet which indicates that the phenoData is read by a function called read.AnnotatedDataFrame. The example at the bottom of ?readExpressionSet shows how the function should be sued. The help page for read.AnnotatedDataFrame is accessible at > ?read.AnnotatedDataFrame The examples on the read.AnnotatedDataFrame page include a peak at the first six lines of the sample file, to provide an idea of appropriate format. The examples can be run with > example(read.AnnotatedDataFrame) If you have not already done so, you might look at the vignette 'An introduction to Biobase and ExpressionSet', accessible with > openVignette() Having said all that, I've made a change to the 'devel' version of Biobase so that only the exprsFile argument is required. This will be available to users of the development version of R after 12:00 PST Saturday, or in the next Bioconductor release. Martin Tiago Lopes <tiagojab at="" yahoo.com.br=""> writes: > Dear Mr. Morgan > first of all, I would like to say that I admire and appreciate your work > towards the creation of useful methods for Bioconductor. > I just started using it and changed from Matlab and Mathematica to a free and > open alternative. > I found the following problems: >> dataset<-readExpressionSet("small.txt") > Error in read.table(filename, sep = sep, header = header, quote = quote,? : > ? argument "filename" is missing, with no default >> dataset<-readExpressionSet("small.txt", exprsArgs=list(sep="\t", quote="")) > Error in read.table(filename, sep = sep, header = header, quote = quote,? : > ? argument "filename" is missing, with no default >> dataset<-readExpressionSet("small.txt", > phenoDataFile=character(0),exprsArgs=list(sep="\t", quote="")) > Error in file(file, "r") : invalid 'description' argument > Unfortunately that means for me that I should still use the deprecated version > of eSet... > I was in doubt if this was a bug or not, and decided to write, and hope this > may be useful. > Kind regards, > Tiago > =========================================== > Tiago Lopes > "Sprechen Sie langsam, baby. Ich lerne Ihre Sprache !" > Max-Delbr?ck Centrum f?r Molekular Medizin > Berlin > =========================================== > > -------------------------------------------------------------------- ---------- > > Gesendet von [[Yahoo! Mail]]. > Dem pfiffigeren Posteingang. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793