[BioC] lumi/Biobase combine and gplots interaction

[Janet Young]

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.

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