[BioC] DESeq estimateDispersions() problem

[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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