Hi
I did install it as suggested.
But again as mentioned it could be due to the version of R. we are
trying to get R updated and will see how things go from there.
Thanks for the assistance
Regards
Elsa
On Nov 16, 4:45 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> I see, so you found a dummy version of EBImage over at R-forge. Now
> it make sense. That is *not* the version you wish to install (the
> message explains why that dummy version exists in the first place).
> Instead, go to Bioconductor and install it. Something like:
>
> source("http://bioconductor.org/biocLite.R";);
> biocLite("EBImage");
>
> As I said before, you may want/need to update your version of R.
>
> /Henrik
>
> On Mon, Nov 15, 2010 at 9:37 PM, Elsa Chacko <elsa.cha...@gmail.com> wrote:
> > Hi
>
> > Sorry I should have posted the error i got :
>
> > Loaded EBImage v9.9.9 (2009-09-10). HOWEVER, DO NOT INSTALL THIS
> > PACKAGE. THIS IS AN EMPTY PACKAGE WITH THE SAME NAME AS AN EXISTING
> > BIOC PACKAGE. THE ONLY PURPOSE OF THIS PACKAGE IS TO PREVENT THE R-
> > FORGE BUILD SERVERS TO HALT THE BUILDING OF AROMA.CORE AND
> > AROMA.AFFYMETRIX. THIS DUMMY PACKAGE WILL NOT BE NEEDED WHEN R-FORGE
> > INCLUDES THE REAL EBIMAGE PACKAGE OR SETS
> > R_check_force_suggests=false.
>
> > Seeing the aroma.affymetrix in the message i wrongly assumed that this
> > is an error message from the aroma package..
>
> > Thanks for the assistance
> > Regards
> > Elsa
>
> > On Nov 16, 4:18 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> > project.org> wrote:
> >> 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 athttp://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.
>
> >> > You received this message because you are subscribed to the Google
> >> > Groups "aroma.affymetrix" group with
> >> > websitehttp://www.aroma-project.org/.
> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> >> > To unsubscribe and other options, go
> >> > tohttp://www.aroma-project.org/forum/
>
> > --
> > 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
> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
--
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
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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