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(libd
ir,"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_Te
stData.A03.CEL",
"Human_PM_TestData.B01.CEL","Human_PM_TestData.B02.CEL","Human_PM_Test
Data.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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