Hi.
On Mon, Nov 15, 2010 at 8:50 PM, Elsa Chacko <elsa.cha...@gmail.com> wrote:
> Hi
>
> I am trying to implement the Vignette: Human exon array analysis
> posted at http://www.aroma-project.org/node/37.
>
> However when i got to the section discussing how to browse spatial
> false-colored images of the residuals,
>
> ae <- ArrayExplorer(rs)
> setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow"))
> process(ae, interleaved="auto", verbose=verbose)
>
> i got the error the EBImage package not loaded.
>
> So i went and installed the EBImage package from bioconductors and now
> i get an error stating that i should not have installed this package.
Where does it say you "should not have installed [the EBImage]
package"? I am not sure I understand.
>
> Any help resolving this is very much appreciated?
Whatever the error EBImage reports, I believe it is independent of the
aroma.affymetrix et al. packages. Because of this, I recommend that
you troubleshoot this without loading aroma.affymetrix, but instead
start a fresh R session and make sure you can load EBImage, e.g.
% R --vanilla
[...]
> library("EBImage");
without errors (warnings are ok). If you get errors here, please ask
for further assistance on the Bioconductor mailing list
[http://bioconductor.org/help/mailing-list/], because that is the
place to find people that can help you with EBImage and other
Bioconductor packages.
Also, it may be that there is not compatible version of EBImage for
your OS/platform. The Bioc experts will let you know if this is the
case.
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
Your installation of R is nearly one year old and considered obsolete;
I recommend that you also update R to the latest R 2.12.0 (preferably
the patched version). Over at Bioconductor, they'll most likely ask
you to do that.
Hope this helps
/Henrik
> x86_64-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>
>> traceback()
> 3: stop(gettextf("no methods for '%s' and no documentation for it as a
> function",
> f), domain = NA)
> 2: .helpForCall(topicExpr, parent.frame())
> 1: `?`(EBImage())
>
>
>
> Regards
> Elsa Chacko
> PhD Student
> Macquarie University.
>
> --
> 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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