[BioC] cdf and probe for HT HG-U133+ PM Array Plate

[cstrato]

Dear An

I have just downloaded from Affymetrix all files and the testdata for 
the array plate in order to test if my package "xps" can handle these 
arrays.

I you want to use xps then here is how to proceed:

1, create root scheme:
 > library(xps)

 > libdir <- "/Volumes/GigaDrive/Affy/libraryfiles"
 > anndir <- "/Volumes/GigaDrive/Affy/Annotation"
 > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"

 > scheme.hthgu133ppm <- 
import.expr.scheme("Scheme_HTHGU133pPM_na27",filedir=scmdir,paste(libdir,"HT_HG-U133_Plus_PM.CDF",sep="/"),paste(libdir,"HT_HG-U133_Plus_PM.probe.tab",sep="/"),paste(anndir,"Version09Feb/HT_HG-U133_Plus_PM.na27.1.annot.csv",sep="/"))

Please note that you need to change the header line of 
"HT_HG-U133_Plus_PM.probe.tab" to:
Probe Set Name    Probe X    Probe Y    Probe Interrogation Position    
Probe Sequence    Target Strandedness
(I have no idea why Affymetrix used a different header in this case)

2, import CEL-files
 > library(xps)

 > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
 > celdir <- "/Volumes/GigaDrive/ChipData/Plate/HT_PM_human_tissue_panel"
 > datdir <- "/Volumes/GigaDrive/CRAN/Workspaces/ROOTData"

# first, import ROOT scheme file
 > scheme.u133ppm <- 
root.scheme(paste(scmdir,"Scheme_HTHGU133pPM_na27.root",sep="/"))

# subset of CEL files to import
 > celfiles <- 
c("Human_PM_TestData.A01.CEL","Human_PM_TestData.A02.CEL","Human_PM_TestData.A03.CEL",
              
"Human_PM_TestData.B01.CEL","Human_PM_TestData.B02.CEL","Human_PM_TestData.B03.CEL")
 > celnames <- 
c("TestDataA01","TestDataA02","TestDataA03","TestDataB01","TestDataB02","TestDataB03")
# import CEL files
 > data.mix.u133ppm <- import.data(scheme.u133ppm, "TestDataHTU133PPM", 
filedir=datdir,celdir=celdir,celfiles=celfiles,celnames=celnames)

3, normalize data
 > library(xps)

### first, load ROOT scheme file and ROOT data file
 > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
 > scheme.u133ppm <- 
root.scheme(paste(scmdir,"Scheme_HTHGU133pPM_na27.root",sep="/"))
 > datdir <- "/Volumes/GigaDrive/CRAN/Workspaces/ROOTData"
 > data.u133ppm <- root.data(scheme.u133ppm, 
paste(datdir,"TestDataHTU133PPM_cel.root",sep="/"))

# RMA
 > data.rma <- 
rma(data.u133ppm,"TestDataHTU133PPM_RMA",tmpdir="",background="pmonly",normalize=T)
 > expr.rma <- validData(data.rma)

As you see, using xps you should be able to process your plate data.

Best regards
Christian
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