[Bioc-devel] Problem with "RGChannelSetExtended" class form minfi

[Mohammad Tanvir Ahamed]

Hi, 


In minfi (1.20.2), in current release version Bioconductor 3.4,  the "RGChannelSetExtended" class is defined as 

> getClass("RGChannelSetExtended") 

Class "RGChannelSetExtended" [package "minfi"] 

Slots: 

Name:       assayData          phenoData         featureData   experimentData  annotation        protocolData  .__classVersion__ 
Class:       AssayData AnnotatedDataFrame  AnnotatedDataFrame            MIAxE   character  AnnotatedDataFrame          Versions 

Extends: 

Class "RGChannelSet", directly 
Class "eSet", by class "RGChannelSet", distance 2 
Class "VersionedBiobase", by class "RGChannelSet", distance 3 
Class "Versioned", by class "RGChannelSet", distance 4 
> 





But in minfi (1.21.5), in the development version Bioconductor 3.5, the "RGChannelSetExtended" class is defined as
> getClass("RGChannelSetExtended") 

Class "RGChannelSetExtended" [package "minfi"] 

Slots: 

Name:  annotation     colData  assays             NAMES  elementMetadata  metadata 
Class:  character   DataFrame  Assays character_OR_NULL       DataFrame      list 

Extends: 
Class "RGChannelSet", directly 
Class "SummarizedExperiment", by class "RGChannelSet", distance 2 
Class "Vector", by class "RGChannelSet", distance 3 

Class "Annotated", by class "RGChannelSet", distance 4 


Now to make a new package, which class definition I need to use ? 
And also , for dependency some other packages (wateRmelon, ChAMP), in their development version  Bioconductor 3.5, still using the old definition of "RGChannelSetExtended".
If so, how to solve the problem ? 


Tanvir Ahamed 

Göteborg, Sweden  |  mashranga at yahoo.com