>>>>> "robert" == Robert Gentleman <rgentlem@jimmy.harvard.edu> writes: robert> seems like enough for a start. robert> If you know of particular formats for different packages, such as robert> genespring then writing specialized, named functions for those robert> would be a good thing Genespring was one that came to mind to me, as well (the GPR file format). I think we've got a GPR reader as part of the semi-aborted work at the Hutch, I'll have to check, which would be useful (come to think of it, I ought to have us write that one, perhaps). MAGEML also comes to mind, especially for exporting to Rosetta. I'm not sure what Research Genetic's Pathways uses for a format, I'll have to check. best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my friday location is usually completely unpredictable.)

which do you think is better 1 a method for exprSet called write 2 a method for exprSet called write.table 3 a method for exprSet call write.exprs 4 a function called write.exprs ? im leaning torwards 2 On Wed, 3 Apr 2002, Robert Gentleman wrote: > On Wed, Apr 03, 2002 at 08:36:35AM -0500, Rafael A. Irizarry wrote: > > i think we need a basic write function for people who dont want to learn > > to much R. especially if they want to import into things like genespring > > etc...ill just write a simple one and put it in Biobase. > > > > Rafael, > I think that is a good idea. If you make it a fairly simple > interface to write.table it shouldn't be too hard > > write.exprs(eset, file="", ...) > write.table(exprs(eset), file, ...) > > > seems like enough for a start. > If you know of particular formats for different packages, such as > genespring then writing specialized, named functions for those > would be a good thing > > > > On Wed, 3 Apr 2002, Laurent Gautier wrote: > > > > > On Tue, Apr 02, 2002 at 01:50:05PM -0500, Rafael A. Irizarry wrote: > > > > is there (or are there plans of writing) a method for the exprSet > > > > class that writes out expression values to a flat file? if not ill put one > > > > in affy. > > > > > > > > _______________________________________________ > > > > Biocore mailing list > > > > Biocore@stat.math.ethz.ch > > > > http://www.stat.math.ethz.ch/mailman/listinfo/biocore > > > > > > > > > > > > > > > I think I saw a related post not too long ago in the bioconductor list. > > > > > > I am not familiar enough with the exprSet to know if everything they include could be dumped in a flat file (sometimes objects can be put in files through serialization). > > > > > > I would be in favor of incitating users to learn a bit of R too... having to solve, or ask how to do, things like 'how do I write expression values from an instance of exprSet in a file ?' appears to me like a good way to do it.... > > > > > > comments ? > > > > > > > > > > > > > > > > > > > > > > > > > > > -------------------------------------------------------------- > > > Laurent Gautier CBS, Building 208, DTU > > > PhD. Student D-2800 Lyngby,Denmark > > > tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > +------------------------------------------------------------------- --------+ > | Robert Gentleman phone : (617) 632-5250 | > | Associate Professor fax: (617) 632-2444 | > | Department of Biostatistics office: M1B28 > | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | > +------------------------------------------------------------------- --------+ >