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

[Sean Davis]

On Fri, Mar 26, 2010 at 9:08 AM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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")

Neeraj, sorry for the misinformation.  Thanks, Jim, for the clarification.

Sean

>>
>> 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
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