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
--
Any help would be great.
Thanks.
Harpreet Kaur Saini
Enright Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
Tel: +44-(0)-1223-492676
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
