[BioC] quantile robust and RMA in xps

[Ben Bolstad]

I'm not seeing any issue with this is in preprocessCore. Perhaps you are
running an old version?


> library(preprocessCore)
> data.int <- matrix(rexp(1000000),ncol=10)
> data.int.norm <- 
+ normalize.quantiles.robust(as.matrix(data.int[,-c(1,2)]), n.remove=1, 
+ remove.extreme='both')
> sessionInfo()
R version 2.9.0 RC (2009-04-10 r48319) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] preprocessCore_1.6.0


> 
> > After that I want to use normalize.quantiles.robust function from  
> > affy (is not available in xps)
> > so I did:
> >
> > data.bg.rma<-attachInten(data.bg.rma)
> > data.int<-intensity(data.bg.rma)
> > detach(package:xps)
> > library(affy)
> > data.int.norm<-normalize.quantiles.robust(as.matrix(data.int[,-c 
> > (1,2)]),n.remove=5,remove.extreme='both')
> >   
> 
> In version R-2.9.0 which I am using, this function has moved to package 
> "preprocessCore" but it seems not to work:
> 
> library(preprocessCore)
> data.int.norm <- 
> normalize.quantiles.robust(as.matrix(data.int[,-c(1,2)]), n.remove=1, 
> remove.extreme='both')
> 
> I get the following error message:
> Error in normalize.quantiles.robust(as.matrix(data.int[, -c(1, 2)]), 
> n.remove = 1, :
> VECTOR_ELT() can only be applied to a 'list', not a 'character
>