[BioC] Problems when access elements in mogene10stprobeset.db

Chao-Jen Wong cwon2 at fhcrc.org
Fri Aug 7 21:31:57 CEST 2009


Hi, Peng

First, it seems very strange to me that you have the makecdfenv pacakge
loaded to your workspace.  As Herve mentioned earlier, when we call up
R, we don't have makecdfenv and its denpendencies (affy, affyio and
preprocessCore) loaded to the workspace.  Can you modify your code
mogeneID.R such that it does sessionInfo() before before loading
mogene10stprobese.db?  For example,


     sessionInfo()
    showMehtod("colnames")
    library(mogene10stprobeset.db)
    sessionInfo()
    showMethod("colnames")

Second, I load the makecdfenv package and found out that a class names
ProbeSet has also obtained the' colnames' method.  I don't know if the
colnames method restricted to the ProbeSet class in makecdfenv package
somehow interferes with 'colnames' for the Bimap class. Below is my code
(in which I tried to use older version of R). Btw, I was able to run
your code using R2.9 and R2.10 with and without having makecdfenv loaded.

library(makecdfenv)
...
> showMethods("colnames")
Function: colnames (package base)
x="ANY"
x="ProbeSet"

library(mogene10stprobeset.db)
...
> showMethods("colnames")
Function: colnames (package base)
x="ANY"
x="AnnDbBimap"
x="FlatBimap"
x="ProbeSet"
sessionInfo()

> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-03-06 r48061)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
[3] DBI_0.2-4                   AnnotationDbi_1.6.1
[5] makecdfenv_1.22.0           affyio_1.11.3
[7] affy_1.22.1                 Biobase_2.4.1

loaded via a namespace (and not attached):
[1] preprocessCore_1.6.0




Peng Yu wrote:
> Hi Hervé,
>
> I even can not run the second command ('showMethods'). The following
> is the screen copy. Could you talk a look what is wrong?
>
> Regards,
> Peng
>
>
> =================start here
> $ R --no-init-file
>
> R version 2.9.1 (2009-06-26)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>   
>> library(mogene10stprobeset.db)
>>     
> Loading required package: AnnotationDbi
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: DBI
>   
>> showMethods("colnames")
>>     
> Error in .showMethodsTable(fdef, includeDefs, inherited, classes = classes,  :
>   trying to get slot "signature" from an object of a basic class
> ("NULL") with no slots
>   
>> sessionInfo()
>>     
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
> [3] DBI_0.2-4                   AnnotationDbi_1.6.1
> [5] Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] affy_1.22.1          affyio_1.12.0        makecdfenv_1.22.0
> [4] preprocessCore_1.6.0
>
> ===================end here
>
> ===================start here again
> $ R --no-init-file
>
> R version 2.9.1 (2009-06-26)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>   
>> sessionInfo()
>>     
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> ==========================end here
>
> 2009/8/6 Hervé Pagès <hpages at fhcrc.org>:
>   
>> Hi Peng,
>>
>> Like Marc, I cannot reproduce this either. I've run your script with
>> Rscript and also interactively. I have exactly the same version of
>> everything as you *except* that you end up with more stuff loaded in
>> your session:
>>
>>  YOU HAVE
>>  --------
>>    other attached packages:
>>      [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>      [3] DBI_0.2-4                   AnnotationDbi_1.6.1
>>      [5] makecdfenv_1.22.0           affyio_1.12.0
>>      [7] affy_1.22.1                 Biobase_2.4.1
>>    loaded via a namespace (and not attached):
>>      [1] preprocessCore_1.6.0
>>
>>  I HAVE
>>  ------
>>    other attached packages:
>>      [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>      [3] DBI_0.2-4                   AnnotationDbi_1.6.1
>>      [5] Biobase_2.4.1
>>
>> How can you end up with those extra packages? Even if I cannot
>> explain how the presence of these packages could be related to
>> the error you get, there is something weird here that you need
>> to investigate.
>>
>> Do you see those extra packages when you run
>>  Rscript --no-init-file mogeneID.R
>>
>> Do you get this error when you run the script interactively?
>> What's your sessionInfo() right after you've started R-2.9.1
>> interactively and loaded mogene10stprobeset.db? Should be the same
>> as mine.
>>
>> It looks like the colnames method for Bimap objects is returning NULL.
>> Or like there is no colnames method for Bimap objects anymore. In that
>> case, calling colnames on the object will also return NULL.
>>
>> Can you please run the following code step by step and see if you get
>> the same output as I do:
>>
>>     
>>> library(mogene10stprobeset.db)
>>> showMethods("colnames")
>>>       
>> Function: colnames (package base)
>> x="AnnDbBimap"
>> x="ANY"
>> x="FlatBimap"
>>
>>     
>>> all_probes<-ls(mogene10stprobesetENTREZID)
>>> set.seed(0xa1beef)
>>> probes <-sample(all_probes, 5)
>>> print(probes)
>>>       
>> [1] "10377734" "10527109" "10489285" "10353981" "10371859"
>>
>>     
>>> x <- mogene10stprobesetENTREZID
>>> colnames(x)
>>>       
>> [1] "probe_id" "gene_id"
>>
>>     
>>> keys(x) <- probes
>>> colnames(x)
>>>       
>> [1] "probe_id" "gene_id"
>>
>>     
>>> Rattribnames(x) <- NULL
>>> colnames(x)
>>>       
>> [1] "probe_id" "gene_id"
>>
>>     
>>> y <- AnnotationDbi:::flatten(x, fromKeys.only=TRUE)
>>> class(y)
>>>       
>> [1] "FlatBimap"
>> attr(,"package")
>> [1] "AnnotationDbi"
>>
>>     
>>> colnames(y)
>>>       
>> [1] "probe_id" "gene_id"
>>
>>     
>>> Rattribnames(y) <- NULL
>>> colnames(y)
>>>       
>> [1] "probe_id" "gene_id"
>>
>> Thanks!
>> H.
>>
>>
>>     
>>> sessionInfo()
>>>       
>> R version 2.9.1 (2009-06-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>> [3] DBI_0.2-4                   AnnotationDbi_1.6.1
>> [5] Biobase_2.4.1
>>
>>
>> Peng Yu wrote:
>>     
>>> Hi,
>>>
>>> I run the following command, which still give me the same error.
>>>
>>> Rscript --no-init-file mogeneID.R
>>>
>>> Can somebody let me know how to figure out what the problems are? Is
>>> there any hiden BioC information that may be shown to pinpoint the
>>> problems?
>>>
>>> Regards,
>>> Peng
>>>
>>> On Thu, Aug 6, 2009 at 4:41 PM, Marc Carlson<mcarlson at fhcrc.org> wrote:
>>>       
>>>> Hi Peng,
>>>>
>>>> I have run the following;
>>>>
>>>> library(mogene10stprobeset.db)
>>>> sessionInfo()
>>>> all_probes<-ls(mogene10stprobesetENTREZID)
>>>> set.seed(0xa1beef)
>>>> probes <-sample(all_probes, 5)
>>>> print(probes)
>>>> mogene10stprobesetENTREZID[[probes[1]]]
>>>>
>>>>
>>>> And it runs fine for me.  So I don't think there is anything wrong with
>>>> your R script, unless there is more than you have shown us here.  The
>>>> one thing I noticed was that my version of R was slightly newer than
>>>> yours.  But a problem like you report here should have alerted a lot
>>>> more people if it were caused by R.
>>>>
>>>>  Marc
>>>>
>>>>
>>>>
>>>> Peng Yu wrote:
>>>>         
>>>>> Hi,
>>>>>
>>>>> Below this email is the R script and the output that I got after
>>>>> running the script. Can somebody take a look help me figure out why I
>>>>> get an error message? I followed in the instructions in
>>>>> AnnotationDbi.pdf.
>>>>>
>>>>> Regards,
>>>>> Peng
>>>>>
>>>>> $ cat mogeneID.R
>>>>> library(mogene10stprobeset.db)
>>>>> sessionInfo()
>>>>> all_probes<-ls(mogene10stprobesetENTREZID)
>>>>> set.seed(0xa1beef)
>>>>> probes <-sample(all_probes, 5)
>>>>> print(probes)
>>>>> mogene10stprobesetENTREZID[[probes[1]]]
>>>>>
>>>>> $ Rscript mogeneID.R
>>>>> Loading required package: methods
>>>>> Loading required package: Biobase
>>>>> Loading required package: utils
>>>>>
>>>>> Welcome to Bioconductor
>>>>>
>>>>>  Vignettes contain introductory material. To view, type
>>>>>  'openVignette()'. To cite Bioconductor, see
>>>>>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>>>
>>>>> Loading required package: affy
>>>>> Loading required package: affyio
>>>>> Loading required package: AnnotationDbi
>>>>> Loading required package: DBI
>>>>> R version 2.9.1 (2009-06-26)
>>>>> x86_64-unknown-linux-gnu
>>>>>
>>>>> locale:
>>>>>
>>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices datasets  utils     methods   base
>>>>>
>>>>> other attached packages:
>>>>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>>>> [3] DBI_0.2-4                   AnnotationDbi_1.6.1
>>>>> [5] makecdfenv_1.22.0           affyio_1.12.0
>>>>> [7] affy_1.22.1                 Biobase_2.4.1
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] preprocessCore_1.6.0
>>>>> [1] "10377734" "10527109" "10489285" "10353981" "10371859"
>>>>> Error in names(colnames) <- colmetanames(x) :
>>>>>  attempt to set an attribute on NULL
>>>>> Calls: [[ ... as.list -> as.list -> .tagCol -> tagname -> tagname
>>>>> Execution halted
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>
>>>>>           
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
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>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>       
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>     
>
> _______________________________________________
> Bioconductor mailing list
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>   


-- 
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org



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