[BioC] Re: writing exprSet to a flat file
Rafael A. Irizarry
rafa@jhu.edu
Wed, 03 Apr 2002 12:33:14 -0500 (EST)
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.
> > > >
> > > > _______________________________________________
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> > > > Biocore@stat.math.ethz.ch
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> > >
> > >
> > >
> > >
> > > 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 |
> | Department of Biostatistics office: M1B28
> | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu |
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