[BioC] DESeq estimateDispersions() problem

[Karl Lundén]

Thanks!
 I am working on the reinstallation.

Karl
Jun 1, 2012 kl. 4:33 PM skrev Nicolas Delhomme:

> Indeed; good catch Steve. Calling the help that way gives me a very similar error to the one you reported:
> 
> ?estimateDispersions()
> Error in .helpForCall(topicExpr, parent.frame()) : 
>  no documentation for function ‘estimateDispersions’ and signature ‘object = "ANY"’
> In addition: Warning message:
> In .helpForCall(topicExpr, parent.frame()) :
>  no method defined for function ‘estimateDispersions’ and signature ‘object = "ANY"’
> 
> whereas this works as expected:
> 
> ?estimateDispersions
> Help on topic ‘estimateDispersions’ was found in the following
> packages:
> 
>  Package               Library
>  DESeq                 /Library/Frameworks/R.framework/Versions/2.15/Resources/library
>  Biobase               /Library/Frameworks/R.framework/Versions/2.15/Resources/library
> <truncated output>
> 
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] C/UTF-8/C/C/C/C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] DESeq_1.8.2        locfit_1.5-8       Biobase_2.16.0     BiocGenerics_0.2.0
> 
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.18.0 DBI_0.2-5            IRanges_1.14.3      
> [4] RColorBrewer_1.0-5   RSQLite_0.11.1       annotate_1.34.0     
> [7] genefilter_1.38.0    geneplotter_1.34.0   grid_2.15.0         
> [10] lattice_0.20-6       splines_2.15.0       stats4_2.15.0       
> [13] survival_2.36-14     xtable_1.7-0
> 
> Cheers,
> 
> Nico
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> Genome Biology Computational Support
> 
> European Molecular Biology Laboratory
> 
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
> 
> 
> 
> 
> 
> On Jun 1, 2012, at 4:06 PM, Steve Lianoglou wrote:
> 
>> Hi Karl,
>> 
>> estimateDispersions is still definitely there ... you can verify that
>> by looking through the the DESeq Reference Manual:
>> 
>> http://bioconductor.org/packages/2.10/bioc/manuals/DESeq/man/DESeq.pdf
>> 
>> It seems there's something wonky going on with your install. As
>> Nicolas said, providing the output from `sessionInfo()` after you load
>> DESeq will be most helpful.
>> 
>> As a side note, I just want to point out that you are trying to invoke
>> the help incorrectly:
>> 
>> On Thu, May 31, 2012 at 8:29 AM, Karl Lundén <karl.lunden at slu.se> wrote:
>> [snip]
>>>> library(DESeq)
>>>> ?estimateDispersions()
>>> Error in .helpForCall(topicExpr, parent.frame()) :
>>> no methods for 'estimateDispersions' and no documentation for it as a function
>> 
>> You should remove the open/close parens. So your call to help should be:
>> 
>> R> ?estimateDispersions
>> 
>> HTH,
>> -steve
>> 
>> -- 
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>> | Memorial Sloan-Kettering Cancer Center
>> | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>> 
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>