Tim: I thought combine() has binary.

Juliet: this often comes up.  You can do
  assign("NAME", object)
which is essentially equivalent to
  NAME <- object
Then you can also get the object by
  get("NAME")

Kasper



On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah <juliet.hannah@gmail.com>wrote:

> Thanks Tim.
>
> I'm trying this out and looks like I did not think this through. So let's
> say I have several CEL files.
>
> I am spreading this out over a cluster. So I have
>
> myFiles = ("cel1.CEL","cel2,CEL")
>
> # pick one file
>
> fileToNormalize = myFiles[fileIndex]
>
> # normalize this to create eset
>
> normalized = SCAN(fileToNormalize)
>
> # create unique output name to save
>
> outFileName <- paste(fileToNormalize,".Rdata",sep="")
>
> save(normalized,file=outFileName)
>
> My problem is now an R one, but related to this problem. "normalized" must
> be given a unique name so that when I load
> all the esets back in they have different names.
>
> Any suggestions?
>
>
>
>
> On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche@gmail.com
> >wrote:
>
> > qux <- combine(foo, bar, baz)
> >
> > if foo, bar, and baz are all ExpressionSets (or other eSets of suitable
> > mien) with the same fData rows and pData columns.
> >
> > I did this the other day for a huge GEO dataset that came as 3 separate
> > Esets off of getGEO.  (Then I turned it into a SummarizedExperiment, of
> > course)
> >
> >
> >
> > On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah@gmail.com
> >wrote:
> >
> >> Thanks Ryan. I'll try this out. What if the esets are already generated.
> >> So
> >> I have a bunch laying
> >> around. I'll look into your answer more and see if I can apply it to
> this
> >> situation.
> >>
> >>
> >> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct@thompsonclan.org
> >> >wrote:
> >>
> >> >    celfiles <- list.files(pattern=".*\\.CEL$"**)
> >>
> >> >    scan.esets <- lapply(celfiles, SCAN)
> >> >    scan.eset <- Reduce(combine, scan.esets)
> >> >
> >> > I forget what package the "combine" function is from, but I assume
> it's
> >> > the same package that provides the ExpressionSet class.
> >> >
> >> >
> >> >
> >> > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote:
> >> >
> >> >> All,
> >> >>
> >> >> SCAN outputs an ExpressionSet object for each CEL file. What is a
> nicer
> >> >> way
> >> >> to put them all into a matrix other than converting each one to a
> >> vector
> >> >> and then cbinding after each conversion?
> >> >>
> >> >> Thanks,
> >> >>
> >> >> Juliet
> >> >>
> >> >>         [[alternative HTML version deleted]]
> >> >>
> >> >> ______________________________**_________________
> >> >> Bioconductor mailing list
> >> >> Bioconductor@r-project.org
> >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor>
> >> >> Search the archives: http://news.gmane.org/gmane.**
> >> >> science.biology.informatics.**conductor<
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor>
> >>
> >> >>
> >> >
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
> >
> > --
> > *He that would live in peace and at ease, *
> > *Must not speak all he knows, nor judge all he sees.*
> > *
> > *
> > Benjamin Franklin, Poor Richard's Almanack<
> http://archive.org/details/poorrichardsalma00franrich>
> >
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

