[BioC] Re: writing exprSet to a flat file

[Rafael A. Irizarry]

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
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> > 
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> 
> -- 
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> | 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   |
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