[BioC] quantile robust and RMA in xps
cstrato at aon.at
Thu May 28 17:15:46 CEST 2009
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))
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 <-
> #Boxplot is NOT ok
> any hint?
>> The new replacement method "intensity()<-" has an option to create a
>> new ROOT file (see?intensity), thus you need to do:
>> 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
>> 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",
>> boxplot(data.mp.rma) #boxplot is now OK.
>> I hope this helps.
>> Best regards
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