Dear Lana Here is the example code and verbose output how to import the pgf and latest Affymetrix annotation file for MoGene: > library(xps) Welcome to xps version 1.2.2 an R wrapper for XPS - eXpression Profiling System (c) Copyright 2001-2008 by Christian Stratowa > libdir <- "/Volumes/GigaDrive/Affy/libraryfiles" > anndir <- "/Volumes/GigaDrive/Affy/Annotation" > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" > scheme.mogene10stv1r3.na27 <- import.genome.scheme("Scheme_MoGene10stv1r3_na27",filedir=scmdir, + paste(libdir,"MoGene-1_0-st-v1.r3.analysis-lib-files/MoGene- 1_0-st-v1.r3.clf",sep="/"), + paste(libdir,"MoGene-1_0-st-v1.r3.analysis-lib-files/MoGene- 1_0-st-v1.r3.pgf",sep="/"), + paste(anndir,"Version08Nov/MoGene- 1_0-st-v1.na27.mm9.transcript.csv",sep="/")) Creating new file </volumes>... Importing </volumes> as <mogene-1_0-st-v1.cxy>... <1102500> records imported...Finished New dataset <mogene-1_0-st-v1> is added to Content... Importing </volumes> as <mogene-1_0-st-v1.ann>... Number of transcripts is <35519>. <35519> records read...Finished <35519> records imported...Finished Importing </volumes> as <mogene-1_0-st-v1.scm>... Reading data from input file... Number of probesets is <35557>. Note: Number of annotated probesets <35519> is not equal to number of probesets <35557>. <35557> records read...Finished Sorting data for probeset_type and position... Total number of controls is <6682> Note: no data for probeset type: control->chip... Filling trees with data for probeset type: normgene, rescue... Filling trees with data for probeset type: control->bgp... Filling trees with data for probeset type: control->affx... <35474> probeset tree entries read...Finished Number of control->affx probesets is <22>. Filling trees with data for probeset type: main... Filling trees with data for non-annotated probesets... <906151> records imported...Finished <35557> total transcript units imported. Genome cell statistics: Number of unit cells: minimum = 4, maximum = 6515 > For more example code how to use the Affymetrix whole Gene arrays, please have a look at scripts "script4xps.R" and "script4exon.R", which are located in directory xps/examples. For Windows specific comments see: https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025 452.html Best regards Christian Lana Schaffer wrote: > Christian, > Now I need to make sure that I can use the pgf and clf files > (not the CDF) for the CEL file import? > Lana > > -----Original Message----- > From: cstrato [mailto:cstrato at aon.at] > Sent: Friday, December 12, 2008 2:42 PM > To: Lana Schaffer > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] installing xps > > Dear Lana > > This is the usual error message you get when you have installed the > wrong root version, because it cannot find the correct version of > libCore.dll. > > You need to install "root_v5.18.00.win32.vc80.msi" which you can > download from: > http://root.cern.ch/root/Version518.html > > Best regards > Christian > > Lana Schaffer wrote: > >> Christian, >> I was unable to locate libCore.dll. >> Where is this file? >> Lana >> >> -----Original Message----- >> From: cstrato [mailto:cstrato at aon.at] >> Sent: Friday, December 12, 2008 1:03 PM >> To: Lana Schaffer >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] installing xps >> >> Dear Lana >> >> This is the most common question of Windows users: >> Since Bioconductor has compiled the Windows version of xps using root >> 5.18.00 you need to install the binary of this version. >> >> Please see also my introductory comments for Windows users: >> https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025 >> 45 >> 2.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 >> _._._._._._._._._._._._._._._._._._ >> >> >> Lana Schaffer wrote: >> >> >>> Hi, >>> I am trying to install xps and get an error message when loading: >>> Error in inDL(x, as.logical(local), as.logical(now), ...) : >>> unable to load shared library >>> 'C:/PROGRA~1/R/R-28~1.0/library/xps/libs/xps.dll': >>> LoadLibrary failure: The specified procedure could not be found. >>> Error: package/namespace load failed for 'xps' >>> >>> I have installed ROOT 5.19.02 from binary. >>> Does this mean that I need to install ROOT from source? >>> >>> >>> >>> >>>> sessionInfo() >>>> >>>> >>>> >>> R version 2.8.0 (2008-10-20) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.8.0 >>> >>> Lana Schaffer >>> Biostatistics/Informatics >>> The Scripps Research Institute >>> DNA Array Core Facility >>> La Jolla, CA 92037 >>> (858) 784-2263 >>> (858) 784-2994 >>> schaffer at scripps.edu >>> >>> _______________________________________________ >>> 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 >>> >>> >>> >>> >>> >> >> >> > > > >