[BioC] quantile robust and RMA in xps

[cstrato]

You are right, my version was 1.4.0, although I thought I have updated 
all packages.
When running the code with 1.6.0 everything is now ok.

Best regards
Christian

Ben Bolstad wrote:
> 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
>>
>>     
>
>
>
>
>