[BioC] backgroundCorrect for RGlist

[Wolfgang Huber]

Dear Harpreet

the "beadarray" and the "limma" package both define generic functions 
"backgroundCorrect", and according to your sessionInfo "beadarray" comes 
earlier in your search path.

When you load "beadarray", do you also get (as I do):

    The following object(s) are masked from package:limma :

          backgroundCorrect,
          imageplot,
          plotMA

As a solution for your problem, you can always call the version of 
backgroundCorrect that you mean by qualifying it with:

   limma::backgroundCorrect

And you can check whether you really need to attach "beadarray" for your 
analysis.

In general, there is no guarantee with R that different user-contributed 
packages do not define the same symbols - hence learning to work with 
namespaces is a good thing for developers, as well as for users.

Best wishes
   Wolfgang

Wolfgang Huber, EBI


Harpreet Kaur Saini ha scritto:
> Hi,
> 
> I am analyzing the two-color array data and for the background correction,
> I am using the backgroundCorrect function.
> 
> RGb<-backgroundCorrect(RG,method="normexp",offset=50).
> 
> where RG is the RGlist.
> 
> I am getting the following error:
> 
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "backgroundCorrect", for
> signature "RGList"
> 
> Here is my sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-apple-darwin8.11.1
> 
> locale:
> C
> 
> attached base packages:
>  [1] grid      splines   tools     stats     graphics  grDevices utils
>  [8] datasets  methods   base
> 
> other attached packages:
>  [1] statmod_1.3.8             MASS_7.2-45
>  [3] Ringo_1.6.0               SparseM_0.78
>  [5] arrayQualityMetrics_1.8.1 marray_1.20.0
>  [7] beadarray_1.10.0          sma_0.5.15
>  [9] hwriter_0.93              latticeExtra_0.5-4
> [11] simpleaffy_2.18.0         affyPLM_1.18.0
> [13] preprocessCore_1.4.0      gcrma_2.14.1
> [15] matchprobes_1.14.1        RColorBrewer_1.0-2
> [17] vsn_3.8.0                 affy_1.20.0
> [19] genefilter_1.22.0         survival_2.34-1
> [21] geneplotter_1.20.0        annotate_1.20.1
> [23] xtable_1.5-4              AnnotationDbi_1.4.2
> [25] lattice_0.17-17           Biobase_2.2.1
> [27] limma_2.16.3
> 
> loaded via a namespace (and not attached):
> [1] DBI_0.2-4          KernSmooth_2.22-22 RSQLite_0.7-1      affyio_1.10.1