[BioC] gdata affects LumiBatch::combine method
Mark Cowley
m.cowley at garvan.org.au
Thu Oct 11 06:53:02 CEST 2012
cheers Martin, that makes sense. as much as i love a bit of recursion, I'll submit a patch to Pan Du & hopefully he can update lumi.
cheers,
Mark
On 11/10/2012, at 3:33 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 10/10/2012 09:25 PM, Mark Cowley wrote:
>> 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
>
> I can replicate that with example(LumiBatch) and then
>
> lumi::combine(example.lumi[,1], example.lumi[,2], example.lumi[,3])
>
> I'd say this was an issue in methods, and the work-around (again!) would be to make the recursion here
>
> > lumi::combine
> nonstandardGenericFunction for "combine" defined from package "BiocGenerics"
>
> function (x, y, ...)
> {
> if (length(list(...)) > 0L) {
> callGeneric(x, do.call(callGeneric, list(y, ...)))
> }
> else {
> standardGeneric("combine")
> }
> }
> <environment: 0x1f53748>
>
> into an iteration:
>
> res = example.lumi[,1]
> for (i in 2:3)
> res = combine(res, example.lumi[,i])
>
> Martin
>
>>
>> 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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>>>
>>>
>>> --
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
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