[BioC] Problems when access elements in mogene10stprobeset.db

Hervé Pagès hpages at fhcrc.org
Fri Aug 7 02:47:49 CEST 2009


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
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>>>
>>>
>>
> 
> _______________________________________________
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> 

-- 
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



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