[BioC] lumi/Biobase combine and gplots interaction

[Janet Young]

thanks, Martin.  

I see - I thought there might be some clever behind-the-scenes method selection going on that paid attention to the class of the objects.  

I'd almost got to your solution:  I'd tried lumi::combine, but I should have realized Biobase::combine would do it.

Janet


On Jul 12, 2011, at 11:30 AM, Martin Morgan wrote:

> On 07/12/2011 11:23 AM, Janet Young wrote:
>> Hi,
>> 
>> I've been using "combine" on lumiBatch objects without problems,
>> until just now when I tried using it after also loading the gplots
>> package.  It looks like the combine function from the gdata package
>> is causing trouble with selecting the right method for combine. For
>> now I just won't load gplots until after I've done my "combine", but
>> I thought you'd want to know.
> 
> Hi Janet --
> 
> R finds the first combine on it's search path search() and there's nothing the developer can do to change that. If gdata and Biobase were frequently used together it might motivate the developers of one package to Depend: or Import: the other and to re-use the same 'combine' generic, but that isn't the case here. Use Biobase::combine(x, y).
> 
> Martin
> 
>> 
>> I think I've included all the useful info below.
>> 
>> thanks very much,
>> 
>> Janet Young
>> 
>> -------------------------------------------------------------------
>> 
>> Dr. Janet Young
>> 
>> Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N.,
>> C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA.
>> 
>> tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung  ...at...
>> fhcrc.org
>> 
>> -------------------------------------------------------------------
>> 
>> 
>> library(lumi) data(example.lumi)
>> 
>> x<- example.lumi y<- example.lumi sampleNames(y)<-
>> paste("y",sampleNames(y), sep="_")
>> 
>> z<- combine(x,y) class(z) ### LumiBatch
>> 
>> library(gdata) ### (combine is masked from Biobase)
>> 
>> z2<- combine(x,y) class(z2) #### data.frame
>> 
>> 
>> sessionInfo()
>> 
>> R version 2.13.1 (2011-07-08) Platform: i386-apple-darwin9.8.0/i386
>> (32-bit)
>> 
>> locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages: [1] grid      stats     graphics  grDevices
>> utils     datasets  methods   base
>> 
>> other attached packages: [1] gplots_2.8.0   caTools_1.12
>> bitops_1.0-4.1 gdata_2.8.1    gtools_2.6.2   lumi_2.4.0 [7]
>> nleqslv_1.8.5  Biobase_2.12.2
>> 
>> loaded via a namespace (and not attached): [1] affy_1.30.0
>> affyio_1.20.0         annotate_1.30.0       AnnotationDbi_1.14.1 [5]
>> DBI_0.2-5             hdrcde_2.15           KernSmooth_2.23-6
>> lattice_0.19-30 [9] MASS_7.3-13           Matrix_0.999375-50
>> methylumi_1.8.0       mgcv_1.7-6 [13] nlme_3.1-101
>> preprocessCore_1.14.0 RSQLite_0.9-4         tools_2.13.1 [17]
>> xtable_1.5-6
>> 
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> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
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> 
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