Thanks to everybody that answer my previous post!!!
I succeed in working creating a root. scheme!!.
RMA run fine but the results have only 57 genes...
Here is my code. Any help will be appreciated.

Thanks

Mayte


library(xps)
### define directories:
# directory containing Affymetrix library files
libdir <- "/Users/Mayte/Rlibrary/AffyDB/libraryfiles"
# directory containing Affymetrix annotation files
anndir <- "/Users/Mayte/Rlibrary/AffyDB/Annotation"
# directory to store ROOT scheme files
scmdir <- "/Users/Mayte/Rlibrary/AffyDB/ROOTSchemes"

  scheme.hugene10stv1r4.na28 <- import.genome.scheme 
("Scheme_HuGene10stv1r4_na28",filedir=scmdir,
                               paste(libdir,"HuGene-1_0-st- 
v1.r4.clf",sep="/"),
                               paste(libdir,"HuGene-1_0-st- 
v1.r4.pgf",sep="/"),
                               paste(anndir,"HuGene-1_0-st- 
v1.na28.hg18.transcript.csv",sep="/"))

scheme.hugene10stv1r4 <- root.scheme(paste(scmdir,  
"Scheme_HuGene10stv1r4_na28.root",sep = "/"))
G1ST_data<-import.data(scheme.hugene10stv1r4, "Pamela_G1ST_dataxps",  
celdir=getwd(), celfiles = thecelfiles, verbose = FALSE)
G1ST_rma_xps <- rma(G1ST_data, filename="Test3RMA",tmpdir="",  
background="antigenomic",normalize=T,exonlevel="metacore+affx")

str(G1ST_rma_xps@data)
data.frame':	57 obs. of  10 variables:



On Apr 7, 2009, at 3:34 PM, cstrato wrote:

> Dear Mayte
>
> Martin was already so kind to answer your question where to find  
> the Affymetrix files.
>
> In general you can select any array you want from:
> http://www.affymetrix.com/products_services/index.affx
>
> Thus, when selecting HuGene array you can download all necessary  
> files from:
> http://www.affymetrix.com/products_services/arrays/specific/ 
> hugene_1_0_st.affx#1_6
>
> Furthermore, you can select the annotation files for e.g. na28 from:
> http://www.affymetrix.com/analysis/downloads/na28/
>
> Please note that release 4 (r4) of the HuGene array converts it to  
> an exon array, see:
> https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-February/ 
> 026472.html
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a           A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
>
>
> Mayte Suarez-Farinas wrote:
>> Hi,
>> I am trying to use xps to work with HuGene 1.0
>> I have already ROOT and xps and I am following
>> their code to create the root scheme. The use of this packages are
>> more laborious that the annotation "ways' for other affychip,
>> but I am doing by best. For what I understand
>> I have to download  HuGene-1_0-st-v1.r4.clf,HuGene-1_0-st-  
>> v1.na28.hg18.transcript.csv
>> and  HuGene-1_0-st-v1.r4.pgf form Affywebsite. I was able to find  
>> the  first two but not the
>> last one. ie: HuGene-1_0-st-v1.r4.pgf
>>
>> any help??
>>
>>
>> scheme.hugene10stv1r3.na27 <- import.genome.scheme  
>> ("Scheme_HuGene10stv1r4_na28",filedir=scmdir,
>>                                paste(libdir,"HuGene-1_0-st-  
>> v1.r4.clf",sep="/"),
>>                                paste(libdir,"HuGene-1_0-st-  
>> v1.r4.pgf",sep="/"),
>>                                paste(anndir,"HuGene-1_0-st-  
>> v1.na28.hg18.transcript.csv",sep="/"))
>>
>> Mayte
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
>>
>>
>>
>


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