>

Dear Christian,
I am sorry I need to bother you gain !
Everything worked fine with the background correction, the quantile  
normalization and the substitution
using function "intensity()<-". When I do the boxplot after this, teh  
data is normalized. Then when I use summarize.rma,
after that the data is not normalized anymore.

intensity(data.bg.rma, "tmp_int2", verbose=TRUE) <- data.int.norm
boxplot(data.bg.rma)                          ## Boxplot is perfect!
setName(data.bg.rma) <- "DataSet"
data.mp.rma <- summarize.rma(data.bg.rma,"tmp_sum_rma",exonlevel="core 
+affx")
boxplot 
(data.mp.rma)                                                      
#Boxplot is NOT ok

any hint?

Best

Mayte


>
> The new replacement method "intensity()<-" has an option to create  
> a new ROOT file (see?intensity), thus you need to do:
>
> library(xps)
> str(data.int)
>
> data.int.norm <- as.data.frame(cbind(data.int[,c(1,2)],data.int.norm))
>
> Here you see that I added the (x,y) coordinates, but it is up to  
> you to make sure that the order is correct.
> I am using cbind() to prevent cycling of the samples, which is what  
> I get when using "data.int[,-c(1,2)]".
>
> Now I can use the replacement method:
>
> intensity(data.bg.rma, "tmp_int2", verbose=TRUE) <- data.int.norm
> str(data.bg.rma)
> boxplot(data.bg.rma) #boxplot is OK
>
> Please note that this will take some time since the background- 
> corrected intensities will first be saved as CEL-files which are  
> then imported into the new ROOT file "tmp_int2_cel.root".
>
> Now you can summarize the data using xps, but you need to replace  
> the setname first:
>
> setName(data.bg.rma) <- "DataSet"
> data.mp.rma <- summarize.rma(data.bg.rma, "tmp_sum_rma",  
> exonlevel="core+affx")
> boxplot(data.mp.rma) #boxplot is now OK.
>
> I hope this helps.
> Best regards
> Christian
>
>

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