[BioC] gdata affects LumiBatch::combine method

Mark Cowley m.cowley at garvan.org.au
Thu Oct 11 06:25:24 CEST 2012


Thanks Martin,
Unfortunately, explicitly specifying lumi::combine seems to interfere with the S4 calling mechanism in an interactive session:

### only lumi
library(lumi)
load("Rmisc/n525.RDa")
load("Rmisc/s217.RDa")
load("Rmisc/s295.RDa")
a <- lumi::combine(s217, n525, s295)
Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : 
  'callGeneric' must be called from a generic function or method

a <- combine(s217, n525, s295)
class(a)
# [1] "LumiBatch"

##### gdata then lumi
library(gdata)
library(lumi)
load("Rmisc/n525.RDa")
load("Rmisc/s217.RDa")
load("Rmisc/s295.RDa")
a <- lumi::combine(s217, n525, s295)
Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : 
  'callGeneric' must be called from a generic function or method

a <- combine(s217, n525, s295)
class(a)
# [1] "LumiBatch"

#### lumi then gdata
library(lumi)
library(gdata)
load("Rmisc/n525.RDa")
load("Rmisc/s217.RDa")
load("Rmisc/s295.RDa")
a <- lumi::combine(s217, n525, s295)
Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : 
  'callGeneric' must be called from a generic function or method

a <- combine(s217, n525, s295)
class(a)
# [1] "data.frame"

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] gdata_2.11.0       lumi_2.8.0         nleqslv_1.9.3     
[4] methylumi_2.2.0    ggplot2_0.9.1      reshape2_1.2.1    
[7] scales_0.2.1       Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] affy_1.34.0           affyio_1.24.0        
 [3] annotate_1.34.1       AnnotationDbi_1.18.1 
 [5] bigmemory_4.2.11      BiocInstaller_1.4.7  
 [7] Biostrings_2.24.1     bitops_1.0-4.1       
 [9] BSgenome_1.24.0       colorspace_1.1-1     
[11] DBI_0.2-5             dichromat_1.2-4      
[13] digest_0.5.2          DNAcopy_1.30.0       
[15] GenomicRanges_1.8.12  genoset_1.6.0        
[17] grid_2.15.1           gtools_2.7.0         
[19] hdrcde_2.16           IRanges_1.14.4       
[21] KernSmooth_2.23-8     labeling_0.1         
[23] lattice_0.20-10       MASS_7.3-20          
[25] Matrix_1.0-6          memoise_0.1          
[27] mgcv_1.7-20           munsell_0.3          
[29] nlme_3.1-104          plyr_1.7.1           
[31] preprocessCore_1.18.0 proto_0.3-9.2        
[33] RColorBrewer_1.0-5    RCurl_1.91-1         
[35] Rsamtools_1.8.6       RSQLite_0.11.1       
[37] rtracklayer_1.16.3    stats4_2.15.1        
[39] stringr_0.6.1         tools_2.15.1         
[41] XML_3.9-4             xtable_1.7-0         
[43] zlibbioc_1.2.0       


Reordering my package loads so that lumi is last, and just using 'combine' works.

cheers,
Mark

On 10/10/2012, at 7:06 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> On 10/08/2012 09:40 PM, Mark Cowley wrote:
>> 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?
> 
> Hi Mark -- unfortunately, this is not easily avoidable. gdata (a CRAN  package) defines its own function combine that masks the version used by lumi and other Bioconductor packages. The work-around is to invoke lumi's combine with, e.g.,
> 
> lumi::combine(x = example.lumi[, 1], y = example.lumi[, 3])
> 
> If gdata were in Bioconductor, we could coerce the author into writing a method for combine, as defined in BiocGenerics. If you were writing a package, then you could importMethodsFrom(lumi, combine) and use combine safely in your own package code whether or not gdata was on the search path.
> 
> Martin
> 
>> 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
>> 
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> 
> 
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