[BioC] gdata affects LumiBatch::combine method

[Mark Cowley]

Dear list,
i'm trying to combine two LumiBatch objects, using the S4 combine("LumiBatch","LumiBatch") method, defined originally in BiocGenerics, and enhanced within lumi.
In a fresh session, with just lumi loaded, everything works fine, i.e. I get a LumiBatch object.
As soon as I load gdata, this breaks the combine method, instead returning a data.frame with very odd dimensions. This is true if I load gdata before, or after lumi. Note that showMethods("lumi") doesn't change after loading gdata. Any ideas?

cheers,
Mark

### lumi, then gdata
> suppressPackageStartupMessages(library(lumi))
Warning messages:
1: found methods to import for function ‘eapply’ but not the generic itself 
2: replacing previous import ‘image’ when loading ‘graphics’ 
> load("Rmisc/n525.RDa")
> load("Rmisc/s295.RDa")
> showMethods("combine")
Function: combine (package BiocGenerics)
x="AnnotatedDataFrame", y="AnnotatedDataFrame"
x="ANY", y="missing"
x="AssayData", y="AssayData"
x="data.frame", y="data.frame"
x="eSet", y="eSet"
x="ExpressionSet", y="LumiBatch"
x="LumiBatch", y="ExpressionSet"
x="LumiBatch", y="LumiBatch"
x="matrix", y="matrix"
x="MethyLumiM", y="MethyLumiM"
x="MethyLumiQC", y="MethyLumiQC"
x="MethyLumiSet", y="MethyLumiSet"
x="MIAME", y="MIAME"

> a <- combine(n525, s295)
> class(a)
[1] "LumiBatch"
attr(,"package")
[1] "lumi"
## the expected output

> suppressPackageStartupMessages(library(gdata))
> showMethods("combine")
Function: combine (package BiocGenerics)
x="AnnotatedDataFrame", y="AnnotatedDataFrame"
x="ANY", y="missing"
x="AssayData", y="AssayData"
x="data.frame", y="data.frame"
x="environment", y="environment"
    (inherited from: x="AssayData", y="AssayData")
x="eSet", y="eSet"
x="ExpressionSet", y="LumiBatch"
x="LumiBatch", y="ExpressionSet"
x="LumiBatch", y="LumiBatch"
x="matrix", y="matrix"
x="MethyLumiM", y="MethyLumiM"
x="MethyLumiQC", y="MethyLumiQC"
x="MethyLumiSet", y="MethyLumiSet"
x="MIAME", y="MIAME"

> a <- combine(n525, s295)
> class(a)
[1] "data.frame"
> 


#### gdata then lumi
> suppressPackageStartupMessages(library(gdata))
> suppressPackageStartupMessages(library(lumi))
Warning messages:
1: found methods to import for function ‘eapply’ but not the generic itself 
2: replacing previous import ‘image’ when loading ‘graphics’ 
> load("Rmisc/n525.RDa")
> load("Rmisc/s295.RDa")
> showMethods("combine")
Function: combine (package BiocGenerics)
x="AnnotatedDataFrame", y="AnnotatedDataFrame"
x="ANY", y="missing"
x="AssayData", y="AssayData"
x="data.frame", y="data.frame"
x="eSet", y="eSet"
x="ExpressionSet", y="LumiBatch"
x="LumiBatch", y="ExpressionSet"
x="LumiBatch", y="LumiBatch"
x="matrix", y="matrix"
x="MethyLumiM", y="MethyLumiM"
x="MethyLumiQC", y="MethyLumiQC"
x="MethyLumiSet", y="MethyLumiSet"
x="MIAME", y="MIAME"

> a <- combine(n525, s295)
> class(a)
[1] "LumiBatch"
attr(,"package")
[1] "lumi"


> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lumi_2.10.0        nleqslv_1.9.4      Biobase_2.18.0     BiocGenerics_0.4.0
[5] gdata_2.12.0      

loaded via a namespace (and not attached):
 [1] affy_1.36.0           affyio_1.26.0         annotate_1.36.0      
 [4] AnnotationDbi_1.20.0  BiocInstaller_1.8.1   colorspace_1.1-1     
 [7] DBI_0.2-5             grid_2.15.1           gtools_2.7.0         
[10] IRanges_1.16.2        KernSmooth_2.23-8     lattice_0.20-10      
[13] MASS_7.3-22           Matrix_1.0-9          methylumi_2.4.0      
[16] mgcv_1.7-21           nlme_3.1-104          parallel_2.15.1      
[19] preprocessCore_1.20.0 RSQLite_0.11.2        stats4_2.15.1        
[22] XML_3.95-0.1          xtable_1.7-0          zlibbioc_1.4.0