[BioC] lumi/Biobase combine and gplots interaction

Janet Young jayoung at fhcrc.org
Tue Jul 12 20:23:38 CEST 2011


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.

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



x <- example.lumi
y <- example.lumi
sampleNames(y) <- paste("y",sampleNames(y), sep="_")

z <- combine(x,y)
### LumiBatch

### (combine is masked from Biobase)

z2 <- combine(x,y)
#### data.frame


R version 2.13.1 (2011-07-08)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

[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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