Dear Christian,

Tx for your answer.

>
> 1. Expression array, PM probes are used for background computation:
> > bg.rma <- bgcorrect (data, "tmp_bg2", method="rma", exonlevel="",  
> select="none", option="pmonly:epanechnikov", params=c(16384))
>


I updated to the last version of xps.
still I get a problem with background correction using either  
bgcorrect or bgcorrect.rma:

library(xps)
scmdir <- "/Users/Mayte/Rlibrary/AffyDB/ROOTSchemes"
scheme.hugene10stv1r4 <- root.scheme(paste(scmdir,  
"Scheme_HuGene10stv1r4_na28.root",sep = "/"))

###########################################
outchip<-c(16,20,21)
G1ST_data2<-import.data(scheme.hugene10stv1r4,  
"MyCEL_dataxps_162021x", celdir=getwd(), celfiles = as.character(PD[-
outchip,'File']), verbose = FALSE)

bg.rma <- bgcorrect.rma (G1ST_data2, "tmp_bg1")
Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’

bg.rma <- bgcorrect (G1ST_data2, "tmp_bg1", method="rma",  
exonlevel="", select="none", option="pmonly:epanechnikov", params=c
(16384))
Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’

Any idea  what is going on??

>
> 1. Expression array, PM probes are used for background computation:
> > bg.rma <- bgcorrect (data, "tmp_bg2", method="rma", exonlevel="",  
> select="none", option="pmonly:epanechnikov", params=c(16384))
>
>

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] tools     stats     graphics  grDevices utils     datasets   
methods   base

other attached packages:
[1] hugene10st.db_1.0.2  RSQLite_0.7-1        DBI_0.2-4             
AnnotationDbi_1.5.18 Biobase_2.2.2        preprocessCore_1.4.0 xps_1.4.3

loaded via a namespace (and not attached):
[1] affy_1.20.2       affyio_1.10.1     annotate_1.20.1    
genefilter_1.22.0 simpleaffy_2.18.0 splines_2.8.1     survival_2.34-1


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