[BioC] Error: could not find function "mixedModel2Fit"

[James W. MacDonald]

Hi Sean and Neeraj,

Sean Davis wrote:
> On Fri, Mar 26, 2010 at 7:14 AM, neeraj rana <kushrn at gmail.com> wrote:
>> hi i am getting follwing error in my analysis.
>>
>>> corfit <- duplicateCorrelation(MA.bn, ndups = 1, block = biolrep)
>> Loading required package: statmod
>> Error: could not find function "mixedModel2Fit"
>> In addition: Warning message:
>> In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return
>> = TRUE,  :
>>  there is no package called 'statmod'
>> i could'nt find any package named statmod..
> 
> Hi, Neeraj.
> 
> You managed to install the limma package without one of it's
> dependencies, it appears.  Perhaps you installed limma using some
> method other than:

The statmod package isn't a dependency; it is a suggested package, so 
isn't installed as a matter of course when using biocLite(). However, 
Sean's suggestion will work just as well to add this package:

biocLite("statmod")

Best,

Jim


> 
> source('http://bioconductor.org/biocLite.R')
> biocLite('limma')
> 
> Try installing limma using the above method.  The statmod package and
> any other dependencies for limma will be installed as well as limma
> and your problem will likely be solved.
> 
> Hope that helps.
> 
> Sean
> 
> P.S.  In the future, be sure to include the output of sessionInfo() in posts.
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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