[BioC] quantile robust and RMA in xps

[cstrato]

Dear Mayte,

Can you please send me your complete code from the beginning, so that I 
can test it.

Especially, did you add the (x,y)-coordinates to data.int.norm:

 > data.int.norm <- as.data.frame(cbind(data.int[,c(1,2)], data.int.norm))

Best regards
Christian


Mayte Suarez-Farinas wrote:
>> 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
>>
>>