On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut@gmail.com> wrote:

> Hi,
>
> So in summary, you use an older version of R than mine, but you get a
> newer version of help page. This is really strange. Can somebody help
> me figure out what the problem is with my R installation?
>

Hi, Peng.  You'll want to look at the section called "Arguments" in the help
file.  That is where the suggestion to look at list.files() comes.  I do not
think there is a problem with your installation, at least not contributing
to the current problem.

Sean


> n Thu, Aug 20, 2009 at 4:51 PM, Benilton Carvalho<bcarvalh@jhsph.edu>
> wrote:
> > Peng,
> >
> > the part that was omitted in your message was:
> >
> > Arguments:
> >
> >     ...: parameters to be passed to 'list.files'
> >
> > and note my sessionInfo() (it's a very old R 2.9.x that I'm running, but
> it
> > doesn't play a role in this case).
> >
> > b
> >
> >> sessionInfo()
> > R version 2.9.0 RC (2009-04-10 r48321)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >
> LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] oligo_1.8.1          preprocessCore_1.6.0 oligoClasses_1.6.0
> > [4] Biobase_2.4.1
> >
> > loaded via a namespace (and not attached):
> > [1] affxparser_1.17.2  affyio_1.12.0      Biostrings_2.11.52 DBI_0.2-4
> > [5] IRanges_1.1.66     splines_2.9.0
> >
> >
> > On Aug 20, 2009, at 6:10 PM, Peng Yu wrote:
> >
> >> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi@gmail.com> wrote:
> >>>
> >>>
> >>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut@gmail.com> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I run the following command. But it only gives the file names. I am
> >>>> wondering if there is a way to get the filename along with the
> >>>> directory name, i.e., 'data/ki10923.CEL', etc.
> >>>>
> >>>> Regards,
> >>>> Peng
> >>>>
> >>>>> list.celfiles('data/')
> >>>>
> >>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL"
> >>>> "ki10928.CEL"
> >>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL"
> >>>> "wt10980.CEL"
> >>>
> >>> Hi, Peng.
> >>>
> >>> Reading the help for list.celfiles(), it suggests that all arguments
> are
> >>> passed along to the list.files().  Reading the help for list.files()
> >>> suggests that including full.names=TRUE will return the information you
> >>> want.
> >>>
> >>> Sean
> >>>
> >>>
> >>
> >> I have checked the help page before I sent the message. But the help
> >> page that I got did not show much information. See below the email. My
> >> sessionInfo is shown below the help page. Is my documentation
> >> outdated? I remember that my R installation was updated only two weeks
> >> ago.
> >>
> >> Regards,
> >> Peng
> >>
> >> list.celfiles             package:oligo             R Documentation
> >>
> >> List CEL/XYS files
> >>
> >> Description:
> >>
> >>    Lists the CEL/XYS files.
> >>
> >> Usage:
> >>
> >>    list.celfiles(...)
> >>
> >> Arguments:
> >>
> >>
> >>
> >> Value:
> >>
> >>    Character vector with the filenames.
> >>
> >> Examples:
> >>
> >>    list.xysfiles()
> >>    list.celfiles()
> >>
> >>
> >>
> >>> sessionInfo()
> >>
> >> R version 2.9.1 (2009-06-26)
> >> x86_64-unknown-linux-gnu
> >>
> >> locale:
> >>
> >>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] oligo_1.8.1          preprocessCore_1.6.0 oligoClasses_1.6.0
> >> [4] Biobase_2.4.1
> >>
> >> loaded via a namespace (and not attached):
> >> [1] affxparser_1.16.0 affyio_1.12.0     Biostrings_2.12.8 DBI_0.2-4
> >> [5] IRanges_1.2.3     splines_2.9.1
> >>
> >> _______________________________________________
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> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
>
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