Dear Chris, Maybe the following information can help you solve your problems: This is my setup: A dual-boot MacBook Pro, 2GB RAM, running Windows XP SP2 where I have installed the following binary versions: - R-2.8.0-win32.exe - root_v5.18.00.win32.vc80.msi - xps_1.2.1.zip Note that root_v5.18.00 is necessary since Bioconductor has compiled xps with this version. You can run xps either from RGui or from Rterm: When using RGui you should set "verbose=FALSE" in all functions, since you will not see any messages anyhow. I would recommend using Rterm with "verbose=TRUE", at least initially to get a feeling what xps does, see the examples below. 1. Import schemes: Since xps uses the original Affymetrix CDF, PGF and annotation files, you have to import these files first. Here is my Rterm session for doing this for HG-U133_Plus_2: > library(xps) Welcome to xps version 1.2.1 an R wrapper for XPS - eXpression Profiling System (c) Copyright 2001-2008 by Christian Stratowa > libdir <- "C:/home/Affy/libraryfiles" > anndir <- "C:/home/Affy/Annotation" > scmdir <- "C:/home/Rabbitus/CRAN/Workspaces/Schemes" > scheme.hgu133p2.na27 <- import.expr.scheme("Scheme_HGU133p2_na27",filedir=scmdir,paste(libdir ,"HG-U133_Plus_2.cdf",sep="/"),paste(libdir,"HG-U133-PLUS_probe.tab",s ep="/"),paste(anndir,"Version08Nov/HG- U133_Plus_2.na27.annot.csv",sep="/")) Creating new file <c: home="" rabbitus="" cran="" workspaces="" schemes="" scheme_hgu133p2_na27.root="">.. . Importing <c: home="" affy="" libraryfiles="" hg-u133_plus_2.cdf=""> as <hg-u133_plus_2.scm>... <1354896> records imported...Finished PM/MM statistics: 5 cells with minimum number of PM/MM pairs: 8 1 cells with maximum number of PM/MM pairs: 69 New dataset <hg-u133_plus_2> is added to Content... Importing <c: home="" affy="" libraryfiles="" hg-u133-plus_probe.tab=""> as <hg-u133_plus_2.prb>... Warning: The following header columns are missing: <serial order=""> <604258> records read...Finished <1354896> records imported...Finished probe info: GC content: minimum GC is <3> maximum GC is <22> Melting Tm: minimum Tm is <51> maximum Tm is <89> Importing <c: home="" affy="" annotation="" version08nov="" hg-u133_plus_2.na27.annot.csv=""> as <hg-u133_plus_2.ann>... Warning: The following header columns are missing: <protein families=""> <protein domains=""> Number of annotated transcripts is <54675>. Warning: Number of transcripts with ambigous annotation is <336> <54675> records imported...Finished > I would recommend to import all necessary schemes and save them in a common system directory. You need not save this R session since you can access every scheme in later R sessions with function root.scheme(). Note that with xps_1.2.1 it is no longer necessary to delete the first 12 lines from the annotation file. All warnings can be ignored, they are caused by changes in the Affymetrix annotation files. 2. Import CEL-files: To show you that xps can easily handle many CEL-files I have imported all 53 CEl-files from the Affymetrix human tissue/mix dataset. Here is the output for RGui: > library(xps) Welcome to xps version 1.2.1 an R wrapper for XPS - eXpression Profiling System (c) Copyright 2001-2008 by Christian Stratowa > scmdir <- "E:/CRAN/Workspaces/Schemes" > scmdir <- "E:/CRAN/Workspaces/Schemes" > celdir <- "E:/ChipData/Exon/HuMixture" > datdir <- "E:/CRAN/Workspaces/ROOTData" > scheme.u133p2 <- root.scheme(paste(scmdir,"Scheme_HGU133p2_na27.root",sep="/")) > Sys.time() [1] "2008-12-07 14:47:20 CET" > data.mix <- import.data(scheme.u133p2, "HuMixAllU133P2", filedir=datdir, celdir=celdir, verbose=FALSE) > Sys.time() [1] "2008-12-07 14:53:45 CET" > As you see, importing 53 CEL-files takes about 7 min. Here is the (partial) output when using Rterm: > library(xps) Welcome to xps version 1.2.1 an R wrapper for XPS - eXpression Profiling System (c) Copyright 2001-2008 by Christian Stratowa > scmdir <- "E:/CRAN/Workspaces/Schemes" > celdir <- "E:/ChipData/Exon/HuMixture" > datdir <- "E:/CRAN/Workspaces/ROOTData" > scheme.u133p2 <- root.scheme(paste(scmdir,"Scheme_HGU133p2_na27.root",sep="/")) > data.mix <- import.data(scheme.u133p2, "HuMixAllU133P2", filedir=datdir, celdir=celdir, verbose=TRUE) Opening file <e: cran="" workspaces="" schemes="" scheme_hgu133p2_na27.root=""> in <read> mode... Creating new file <e: cran="" workspaces="" rootdata="" hutissuesu133p2_cel.root="">... Importing <e: chipdata="" exon="" humixture="" u1332plus_ivt_breast_a.cel=""> as <u1332plus_ivt_breast_a.cel>... <1354896> records imported... hybridization statistics: 4 cells with minimal intensity 32 1 cells with maximal intensity 16261 New dataset <dataset> is added to Content... Importing <e: chipdata="" exon="" humixture="" u1332plus_ivt_breast_b.cel=""> as <u1332plus_ivt_breast_b.cel>... <1354896> records imported... hybridization statistics: 1 cells with minimal intensity 24 1 cells with maximal intensity 20496 ... ... Importing <e: chipdata="" exon="" humixture="" u1332plus_ivt_thyroid_b.cel=""> as <u1332plus_ivt_thyroid_b.cel>... <1354896> records imported... hybridization statistics: 1 cells with minimal intensity 29 1 cells with maximal intensity 47017 Importing <e: chipdata="" exon="" humixture="" u1332plus_ivt_thyroid_c.cel=""> as <u1332plus_ivt_thyroid_c.cel>... <1354896> records imported... hybridization statistics: 1 cells with minimal intensity 24 2 cells with maximal intensity 65534 > As you see, in Rterm you see the progress status and get some statistical information. Since CEL-files have often long and strange names I would recommend to use parameter "celnames" in function import.data() to use new names. Once again you need not save the R session since you can access the data in later R sessions using function root.data(). 3. RMA normalization: RMA normalization of all 53 CEL-files takes about 1 hr. Here is the RGui session: > library(xps) Welcome to xps version 1.2.1 an R wrapper for XPS - eXpression Profiling System (c) Copyright 2001-2008 by Christian Stratowa > scmdir <- "E:/CRAN/Workspaces/Schemes" > scheme.u133p2 <- root.scheme(paste(scmdir,"Scheme_HGU133p2_na27.root",sep="/")) > datdir <- "E:/CRAN/Workspaces/ROOTData" > data.u133p2 <- root.data(scheme.u133p2, paste(datdir,"HuMixAllU133P2_cel.root",sep="/")) > Sys.time() [1] "2008-12-07 14:59:12 CET" > data.rma <- rma(data.u133p2,"MixAllU133P2RMA",tmpdir="",background="pmonly",normal ize=TRUE,verbose=FALSE) > Sys.time() [1] "2008-12-07 15:55:25 CET" > In comparison, here is the (partial) Rterm session: > library(xps) Welcome to xps version 1.2.1 an R wrapper for XPS - eXpression Profiling System (c) Copyright 2001-2008 by Christian Stratowa > scmdir <- "E:/CRAN/Workspaces/Schemes" > scheme.u133p2 <- root.scheme(paste(scmdir,"Scheme_HGU133p2_na27.root",sep="/")) > datdir <- "E:/CRAN/Workspaces/ROOTData" > data.u133p2 <- root.data(scheme.u133p2, paste(datdir,"HuMixAllU133P2_cel.root",sep="/")) > Sys.time() [1] "2008-12-07 13:32:35 CET" > data.rma <- rma(data.u133p2,"MixAllU133P2RMA",tmpdir="",background="pmonly",normal ize=TRUE,verbose=TRUE) Creating new file <e: cran="" workspaces="" exon="" hutissues="" u133p2="" mixallu133p2rma.root="">... Opening file <e: cran="" workspaces="" schemes="" scheme_hgu133p2_na27.root=""> in <read> mode... Opening file <e: cran="" workspaces="" rootdata="" humixallu133p2_cel.root=""> in <read> mode... Preprocessing data using method <preprocess>... Background correcting raw data... calculating background for <u1332plus_ivt_breast_a.cel>... background statistics: 750638 cells with minimal intensity 0 1468 cells with maximal intensity 69.3196 calculating background for <u1332plus_ivt_breast_b.cel>... background statistics: 750638 cells with minimal intensity 0 1334 cells with maximal intensity 68.3009 ... ... calculating background for <u1332plus_ivt_thyroid_b.cel>... background statistics: 750638 cells with minimal intensity 0 295 cells with maximal intensity 65.6557 calculating background for <u1332plus_ivt_thyroid_c.cel>... background statistics: 750638 cells with minimal intensity 0 1 cells with maximal intensity 74.3142 Normalizing raw data... normalizing data using method <quantile>... finished filling <53> arrays. .. finished filling <53> trees. cqu>... Converting raw data to expression levels... summarizing with <medianpolish>... calculating expression for <54675> of <54684> units...Finished. expression statistics: minimal expression level is <2.65147> maximal expression level is <15470.9> preprocessing finished. Opening file <e: cran="" workspaces="" schemes="" scheme_hgu133p2_na27.root=""> in <read> mode... Opening file <e: cran="" workspaces="" exon="" hutissues="" u133p2="" mixallu133p2rma.root=""> in <read> mode... Exporting data from tree <*> to file <e: cran="" workspaces="" exon="" hutissues="" u133p2="" mixallu133p2rma.txt="">... Reading entries from <hg-u133_plus_2.ann> ...Finished <54675> of <54675> records exported. > Sys.time() [1] "2008-12-07 14:35:09 CET" > Once again, in Rterm you see the progress status and get some statistical information. I consider it helpful to see the progress information, especially when computation takes a long time. I hope that this demonstration could show you how to use xps successfully, and can help you solving your problems. Best regards Christian cstrato wrote: > Dear Chris > > This is strange, could you please give your sessionInfo(), which > version of xps, which version of ROOT, which version of R, WinXP or > Vista? > > Could you please give the complete code for creating the scheme. > I am not sure if it is a good idea to save the "hgu133plu2.root" file > in the package directory, I would propose to create a directory > "schemes" somewhere else, e.g. "McMasters/schemes". > > Furthermore, could you please set "verbose=TRUE" in the methods and > start R from the Command Console. Then you will see the progress > messages. Could you please send me this output, so that I can check > the result? > > Handling 40 CEL-files should not be a problem, one user of xps > reported that he could successfully handle 500 CEL-files on his > Windows machine. > > 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 > _._._._._._._._._._._._._._._._._._ > > > > Christopher N Barnes wrote: >> All, >> >> I am new to xps and am having trouble reading in the cel files. >> >> I got the 3 correct files from affymetrix and created a scheme >> removing the first 12 lines from the annotation file (fix 1) >> >> >> I then read in my scheme: >> hgu133plus2<-root.scheme(paste(.path.package("xps"),"schemes/hgu133 plus2.root", >> >> sep="/")) >> >> and then try to read in the CEL files. >> celdir2<-"C:/McMasters/test" >> data.test3<-import.data(hgu133plus2,"tmp2",celdir=celdir2, >> verbose=FALSE) >> It worked 1 time and now causes R to crash. I am trying to read in >> 40 CEL files 50,000+ genes on a 4G machine. >> >> Does anyone have any suggestions of another method to read a large >> amount of CEL files. If I try using Read Affy() to read in, I don't >> have the space to allocate. >> Thanks for the Help, >> >> Chris Barnes >> PhD student University of Louisville >> >> [[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 >> >> >> > > _______________________________________________ > 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 > >