[BioC] Re: writing exprSet to a flat file

[Robert Gentleman]

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.
> > > 
> > > _______________________________________________
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> > > 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
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> > 
> 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
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