[Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called From A Package

[Dario Strbenac]

Thank you. I made that change to the edgeR source code and reinstalled it, but I get another error further in my function :

Error in UseMethod("glmFit") : 
  no applicable method for 'glmFit' applied to an object of class "c('DGEList', 'list', 'LargeDataObject', 'vector')"

This is because of LargeDataObject from limma is not imported into edgeR. Can you add that one, too ?
 

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia

________________________________________
From: Gordon K Smyth <smyth at wehi.EDU.AU>
Sent: Friday, 27 June 2014 9:32 AM
To: Dario Strbenac
Cc: bioc-devel at r-project.org
Subject: edgeR estimateGLMRobustDisp Fails when Called From A Package

> Date: Thu, 26 Jun 2014 04:00:11 +0000
> From: Dario Strbenac <dstr7320 at uni.sydney.edu.au>
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called
>       From A  Package
>
> Hello,
>
> I am writing a package that has a function that uses estimateGLMRobustDisp, leading to an error :
>
> Error in dispBinTrend(y, design, offset = offset, method.trend = "loess",  :
>  could not find function "loessFit"
> Calls: edgeRselection ... estimateGLMTrendedDisp -> estimateGLMTrendedDisp.default -> dispBinTrend
>
> I import estimateGLMRobustDisp from edgeR in my NAMESPACE file. This
> error is because edgeR depends on limma, rather than importing from it.
> I want to avoid using parent.env<- and .onLoad to get around the
> problem. Is there any hope of modifying the edgeR description file to
> have limma in the Imports field ?

Nope, because that is neither necessary nor good programming practice
(according to R core).

I will however add loessFit to importFrom() in edgeR's NAMESPACE, which I
think will solve your problem.

Best wishes
Gordon

> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
> ------------------------------

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