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.
You received this message because you are subscribed to the Google Groups
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