Hi Pierre,
I just tried it and it worked. Thanks for the suggestion.
Fong
On Mar 14, 3:28 pm, Pierre Neuvial <pie...@stat.berkeley.edu> wrote:
> Hi Fong,
>
> The standard way to do this within the Aroma framework is to use
> *links* to the directories you need. The best way to do this depends
> on your OS, but in general this can be done within R using the
> function 'createLink' (from R.utils), e.g.:
>
> createLink(target="~/Data/annotationData")
> createLink(target="~/Data/rawData")
>
> will create in the working directory a link to "~/Data/annotationData"
> called "annotationData", and a link to "~/Data/rawData" called
> "rawData".
>
> In general I think that it is very sound to separate the actual
> location of the data from the location of your scripts, and that's
> exactly what you can do with links.
>
> Note that if you'd like the results of your analyses to be written in
> your usual data directory ("~/Data" in the above example) instead of
> your current working directory, then you will also have to do
> something like
>
> createLink(target="~/Data/probeData")
> createLink(target="~/Data/plmData")
>
> Hope this helps,
>
> Pierre
>
> On Mon, Mar 14, 2011 at 7:09 PM, Fong <fongchunc...@gmail.com> wrote:
> > Hi,
>
> > Is there a way to use aroma affymetrix code without having to be in
> > the aroma affymetrix directory? When I am outside of the aroma
> > affymetrix directory and I try to enter the command:
>
> >> cdf <- AffymetrixCdfFile$byChipType('HG-U133_Plus_2', tags='ense')
> > Error in list(`AffymetrixCdfFile$byChipType("HG-U133_Plus_2", tags =
> > "ense")` = <environment>, :
>
> > [2011-03-14 10:56:12] Exception: Could not locate a file for this chip
> > type: HG-U133_Plus_2,ense
> > at throw(Exception(...))
> > at throw.default("Could not locate a file for this chip type: ",
> > paste(c(chipT
> > at throw("Could not locate a file for this chip type: ",
> > paste(c(chipType, tag
> > at method(static, ...)
> > at AffymetrixCdfFile$byChipType("HG-U133_Plus_2", tags = "ense")
>
> > All this code is in a R script and the easy solution would be to set
> > the directory to that be the aroma affymetrix directory using
> > setwd(). But I was wondering if there was some aroma affymetrix shell
> > variable I could set so that it knows where to look for the aroma
> > affymetrix files without having to explicitly set the directory. I
> > haven't been able to find any references to this in the forums.
>
> > Thanks,
>
> > Fong
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
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>
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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