Hi everybody.

I am working with xps and I have to admit I still dont get all the  
nuances, but I am trying my best.
To summarize the data, I want to use rma but with an alteration to  
the normalization step.
so I need to do the 3 steps: bgcorrect, normalize and summarize. I  
got two problems trying to do so:

1. In background correction:

the default RMA background is:
data.bg.rma <- bgcorrect 
(G1ST_data2,"tmp_bg",method="rma",exonlevel="core+affx",  
select="none", option="pmonly:epanechnikov",params=c(16384))
but I got the following error:

g.rma <- bgcorrect(G1ST_data2,"tmp_bg",method="rma",exonlevel="all",  
select="none", 	option="pmonly:epanechnikov",params=c(16384))
Error in .local(object, ...) : error in function ‘BgCorrect’
Opening file </Users/Mayte/Rlibrary/AffyDB/ROOTSchemes/ 
Scheme_HuGene10stv1r4_na28.root> in <READ> mode...
Creating new temporary file </Volumes/..../tmp_bg.root>...
Preprocessing data using method <adjustbgrd>...
    Background correcting raw data...
       calculating background for <1_HuGene 1_0 ST_050409.cel>...
Error: Number of PMs or MMs is zero.
An error has occured: Need to abort current process.

So, I try:

data.bg.rma <- bgcorrect 
(G1ST_data2,"tmp_bg2",method="rma",exonlevel="core+affx",  
select="antigenomic", option="pmonly:epanechnikov",params=c(16384))

which works OK but I dont know if it is OK.
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')

which shows that the data is normalized. Then I have to update the  
intensitities in the xps object data.bg.rma,
which I did and after

library(xps)
str(data.int)
data.int[,-c(1,2)]<-data.int.norm
intensity(data.bg.rma)<-data.int
boxplot(data.bg.rma)              #boxplot is OK

The problem comes when I sumarized the resulting data using median  
polish,
the resulting data is not normalized:

data.mp.rma <- summarize.rma(data.bg.rma,"tmp_sum_rma",exonlevel="core 
+affx")
boxplot(data.mp.rma)    #boxplot is not OK.

I dont know if I make a mistake specially in updating the intensities  
after the normalization step. I will really appreciate any insight on  
this. Below is my session info...


 > sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
  [1] xps_1.2.10                affy_1.20.2                
arrayQualityMetrics_1.8.1 marray_1.20.0              
latticeExtra_0.5-4        vsn_3.8.0
  [7] beadarray_1.10.0          sma_0.5.15                 
hwriter_1.0               affycoretools_1.14.1       
annaffy_1.14.0            KEGG.db_2.2.5
[13] biomaRt_1.16.0            GOstats_2.8.0              
Category_2.8.4            RBGL_1.18.0                
GO.db_2.2.5               RSQLite_0.7-1
[19] DBI_0.2-4                 graph_1.20.0               
limma_2.16.5              affyQCReport_1.20.0        
geneplotter_1.20.0        annotate_1.20.1
[25] AnnotationDbi_1.5.18      lattice_0.17-17            
RColorBrewer_1.0-2        affyPLM_1.18.1             
preprocessCore_1.4.0      xtable_1.5-4
[31] simpleaffy_2.18.0         gcrma_2.14.1               
matchprobes_1.14.1        genefilter_1.22.0          
survival_2.34-1           Biobase_2.2.2

loaded via a namespace (and not attached):
[1] GSEABase_1.4.0     KernSmooth_2.22-22 RCurl_0.94-1        
XML_2.1-0          affyio_1.10.1      cluster_1.11.11



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