[BioC] Missing GeneSymbol and Name information in TopTable
Kai Treuner
ktreuner at braincellsinc.com
Wed Aug 26 20:42:06 CEST 2009
Hi Marc,
Thanks again for checking... As a workaround I do a batch query in
NetAffy to retrieve the gene symbol and gene name information. Oddly
enough it used to work before with a previous install on a different
laptop.
The main issue is still the same warning message (see below) even though
the annotation file has been uploaded and should be available. This also
causes an error when using the gene labeling options with the M A plot
function.
Kai
Warning messages:
1: In getDependencies(pkgs, dependencies, available, lib) :
package 'hgu133plus2' is not available
2: In getDependencies(pkgs, dependencies, available, lib) :
package 'hgu133plus2' is not available
3: In getDependencies(pkgs, dependencies, available, lib) :
package 'hgu133plus2' is not available
> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tcltk stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] tkrplot_0.0-18 hgu133plus2cdf_2.4.0 hgu133plus2.db_2.2.11
[4] RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.6.1
[7] affylmGUI_1.18.0 affyio_1.12.0 affy_1.22.1
[10] Biobase_2.4.1 limma_2.18.2
loaded via a namespace (and not attached):
[1] preprocessCore_1.6.0 tools_2.9.1
-----Original Message-----
From: Marc Carlson [mailto:mcarlson at fhcrc.org]
Sent: Wednesday, August 26, 2009 10:09 AM
To: Kai Treuner
Cc: Bioconductor list list
Subject: Re: [BioC] Missing GeneSymbol and Name information in TopTable
Hi Kai,
All the messages you report for sessionInfo() now look ok to me. I can
only speculate that this might be an issue with affylmGUI. Since this
is a GUI, I am afraid that you will have to tell use very, very
precisely what you do to produce the problem in order for us to try to
help you. The sessionInfo() only tells us what packages you had loaded
(and R version) when you called sessionInfo(), but it seems you are
doing something else that we cannot reproduce without some more
information.
Marc
Kai Treuner wrote:
> Hi Marc,
>
> It still doesn't show the gene symbols or names, here is the code and
> session info from my last analysis:
>
> library("hgu133plus2.db")
> library(affylmGUI)
> history()
>
>
>> sessionInfo()
>>
> R version 2.9.1 (2009-06-26)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tcltk stats graphics grDevices utils datasets
methods
>
> [8] base
>
> other attached packages:
> [1] hgu133plus2cdf_2.4.0 tkrplot_0.0-18 affylmGUI_1.18.0
> [4] affyio_1.12.0 affy_1.22.1 limma_2.18.2
> [7] hgu133plus2.db_2.2.11 RSQLite_0.7-2 DBI_0.2-4
> [10] AnnotationDbi_1.6.1 Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] preprocessCore_1.6.0 tools_2.9.1
>
> It seems there is still a software package missing or not running
> properly?
> Thanks again,
> Kai
>
> -----Original Message-----
> From: Marc Carlson [mailto:mcarlson at fhcrc.org]
> Sent: Friday, August 21, 2009 11:12 AM
> Cc: Kai Treuner; Bioconductor list list
> Subject: Re: [BioC] Missing GeneSymbol and Name information in
TopTable
>
> Hi Kai,
>
> What happens if you just type:
>
> library("hgu133plus2.db")
>
> To load the library before you run whatever it is that you are
running?
>
> Also, history() should display the code from your session. Which you
> could then post so that the rest of us would know what you were trying
> to do.
>
>
> Marc
>
>
>
> Kai Treuner wrote:
>
>> Hi Marc,
>> I went ahead and downloaded the "hgu133plus2.db" package again:
>>
>> package 'hgu133plus2.db' successfully unpacked and MD5 sums checked
>> updating HTML package descriptions
>>
>> However, here is still the same session info:
>>
>> R version 2.9.1 (2009-06-26)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] tcltk stats graphics grDevices utils datasets
>>
> methods
>
>> [8] base
>>
>> other attached packages:
>> [1] tkrplot_0.0-18 hgu133plus2cdf_2.4.0 affylmGUI_1.18.0
>> [4] affyio_1.12.0 affy_1.22.1 Biobase_2.4.1
>> [7] limma_2.18.2
>>
>> loaded via a namespace (and not attached):
>> [1] preprocessCore_1.6.0 tools_2.9.1
>> Warning messages:
>> 1: In getDependencies(pkgs, dependencies, available, lib) :
>> package 'hgu133plus2' is not available
>> 2: In getDependencies(pkgs, dependencies, available, lib) :
>> package 'hgu133plus2' is not available
>>
>>
>> Which command would show the code?
>> Kai
>>
>>
>>
>>
>> -----Original Message-----
>> From: Marc Carlson [mailto:mcarlson at fhcrc.org]
>> Sent: Friday, August 21, 2009 9:33 AM
>> To: Kai Treuner
>> Cc: Sean Davis; bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] Missing GeneSymbol and Name information in
>>
> TopTable
>
>> Hi Kai,
>>
>> I still don't see your code, but just from your sessionInfo(), it
does
>> not appear that you really have the "hgu133plus2.db" package loaded.
>> And as you noted in your previous post, it appears that this is what
>>
> the
>
>> error message is asking about.
>>
>>
>> Marc
>>
>>
>>
>>
>> Kai Treuner wrote:
>>
>>
>>> Hi Sean,
>>>
>>> Here is the session info. Am I missing a specific package to get the
>>> Gene Symbols and names?
>>>
>>> Thanks, Kai
>>>
>>>
>>>
>>> R version 2.9.1 (2009-06-26)
>>>
>>> i386-pc-mingw32
>>>
>>>
>>>
>>> locale:
>>>
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>>
>>>
>>> attached base packages:
>>>
>>> [1] tcltk stats graphics grDevices utils datasets
>>>
>>>
>> methods
>>
>>
>>> [8] base
>>>
>>>
>>>
>>> other attached packages:
>>>
>>> [1] tkrplot_0.0-18 hgu133plus2cdf_2.4.0 affylmGUI_1.18.0
>>>
>>> [4] affyio_1.12.0 affy_1.22.1 Biobase_2.4.1
>>>
>>> [7] limma_2.18.2
>>>
>>>
>>>
>>> loaded via a namespace (and not attached):
>>>
>>> [1] preprocessCore_1.6.0 tools_2.9.1
>>>
>>>
>>>
>>> ________________________________
>>>
>>> From: Sean Davis [mailto:seandavi at gmail.com]
>>> Sent: Thursday, August 20, 2009 5:55 PM
>>> To: Kai Treuner
>>> Cc: bioconductor at stat.math.ethz.ch
>>> Subject: Re: [BioC] Missing GeneSymbol and Name information in
>>>
>>>
>> TopTable
>>
>>
>>>
>>> On Thu, Aug 20, 2009 at 8:15 PM, Kai Treuner
>>> <ktreuner at braincellsinc.com> wrote:
>>>
>>> Hi,
>>> I am trying to get the gene symbols and names of genes included in
>>>
> the
>
>>> TopTable. I am using affylmGUI package under R 2.9.1 on windows XP.
>>>
>>>
>> Even
>>
>>
>>> after downloading the hgu133plus2.db annotation file as well as the
>>> annotate, annaffy and other packages it doesn't work.
>>>
>>> These are the error messages:
>>> Error in text(A[topGenes],M[topGenes], labels=
>>>
>>>
>> substr(genelist[topGenes,
>>
>>
>>> : object 'topGenes' not found
>>>
>>> Warning messages:
>>> 1: In getDependencies(pkgs, dependencies, available, lib) :
>>> package 'hgu133plus2' is not available
>>> 2: In getDependencies(pkgs, dependencies, available, lib) :
>>> package 'hgu133plus2' is not available
>>>
>>>
>>> Hi, Kai.
>>>
>>> You'll want to give the code that you are using for your analysis as
>>> well as the output of sessionInfo().
>>>
>>> Sean
>>>
>>>
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
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>>
>>
>>>
>>>
>>>
>>
>>
>
>
>
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