[BioC] xps and RMA

[cstrato]

Dear Mayte

Please read the following thread and my answers:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-February/026358.html

As I mentioned already, 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

This mail contains the code to use to create the scheme for HuGene and 
for doing rma analysis, i.e. you need to download also the probeset 
annotation file from Affymetrix and use function "import.exon.scheme()" 
to create the scheme.
Alternatively, you could download the old release 3 (r3) files from 
Affymetrix and use "import.genome.scheme()".

Best regards
Christian


Mayte Suarez-Farinas wrote:
> 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 at 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 at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/ 
>>> gmane.science.biology.informatics.conductor
>>>
>>>
>>>
>>>       
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>