[aroma.affymetrix] EBImage issue

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[aroma.affymetrix] EBImage issue

Elsa Chacko
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.

Any help resolving this is very much appreciated?

> sessionInfo()
R version 2.10.1 (2009-12-14)
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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Re: [aroma.affymetrix] EBImage issue

Henrik Bengtsson-4
Hi.

On Mon, Nov 15, 2010 at 8:50 PM, Elsa Chacko <[hidden email]> 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.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://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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[aroma.affymetrix] Re: EBImage issue

Elsa Chacko
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 <[hidden email]> 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 [hidden email]
> > 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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Re: [aroma.affymetrix] Re: EBImage issue

Henrik Bengtsson-4
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 <[hidden email]> 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 <[hidden email]>
>> 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 [hidden email]
>> > 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/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://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/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
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[aroma.affymetrix] Re: EBImage issue

Elsa Chacko
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 <[hidden email]> 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 <[hidden email]>
> >> 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 [hidden email]
> >> > 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 [hidden email]
> > 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/.
To post to this group, send email to [hidden email]
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Re: [aroma.affymetrix] Re: EBImage issue

Henrik Bengtsson-4
On Mon, Nov 15, 2010 at 9:55 PM, Elsa Chacko <[hidden email]> wrote:
> Hi
>
> I did install it as suggested.

Ok, so you still get that message?   Then try to uninstall the dummy
EBImage by first doing:

remove.packages("EBImage");

and assert that it is truly removed by calling library("EBImage") -
you should get an error.

Then restart R, and try to install from Bioconductor.

/Henrik

> 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 <[hidden email]> 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 <[hidden email]>
>> >> 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 [hidden email]
>> >> > 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 [hidden email]
>> > 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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--
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