[BioC] quantile robust and RMA in xps

[cstrato]

Dear Mayte

For HuGene arrays parameter exonlevel must have one of the values 
described in "?exonLevel", for example exonlevel="core+affx". Setting 
exonlevel="" is necessary for expression arrays but not allowed for 
HuGene arrays.

The correct background setting for your case is the one you have used 
initially:
data.bg.rma <- bgcorrect(G1ST_data2, "tmp_bg2" ,method="rma", 
exonlevel="core+affx", select="antigenomic", 
option="pmonly:epanechnikov", params=c(16384))

Best regards
Christian


Mayte Suarez-Farinas wrote:
> 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  
>