Dear James, I have tried to install the MarGene1.0st library file as per the R script mentioned at https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html. However while doing this, an error message has come as "Error in getClass(Class, where = topenv(parent.frame())) : “AffyGenePDInfoPkgSeed” is not a defined class". The output along with the R script is given below for your reference. Kindly suggest how to overcome this error message to load the MarGene 1.0st library files Output message: > source("http:/bioconductor.org/biocLite.R") Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'http:/bioconductor.org/biocLite.R': Invalid argument > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help > baseDir <- "C:/Users/DR.DKDAS/Downloads/CD_MarGene-1_0-st_rev01/Full/MarGene-1_0-st/LibFiles" > (pgf <- list.files(baseDir, pattern = "MarGene-1_0-st.pgf", + full.names = TRUE)) [1] "C:/Users/DR.DKDAS/Downloads/CD_MarGene-1_0-st_rev01/Full/MarGene-1_0-st/LibFiles/MarGene-1_0-st.pgf" > (clf <- list.files(baseDir, pattern = "MarGene-1_0-st.clf", full.names = TRUE)) [1] "C:/Users/DR.DKDAS/Downloads/CD_MarGene-1_0-st_rev01/Full/MarGene-1_0-st/LibFiles/MarGene-1_0-st.clf" > (prob <- list.files(baseDir, pattern = "MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv", full.names = TRUE)) [1] "C:/Users/DR.DKDAS/Downloads/CD_MarGene-1_0-st_rev01/Full/MarGene-1_0-st/LibFiles/MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv" > mps <- list.files(baseDir, pattern = "MarGene-1_0-st.mps$", full.names = TRUE) > trans <- list.files(baseDir, pattern="MarGene-1_0-st-v1.na33.2.caljac3.transcript",full.names=TRUE) > seed <- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = clf, coreMps=mps, transFile=trans, probeFile = prob, author = "Kamila Naxerova", + email = "dasd at nirrh.res.in",biocViews = "AnnotationData",organism = "Marmoset", species = "Callithrix jacchus") Error in getClass(Class, where = topenv(parent.frame())) : “AffyGenePDInfoPkgSeed” is not a defined class > seed <- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = clf, coreMps=mps, transFile=trans, probeFile = prob, author = "Dhanjit", + email = "dasd at nirrh.res.in",biocViews = "AnnotationData",organism = "Marmoset", species = "Callithrix jacchus") makePdInfoPackage(seed, destDir = "C:/Dhanjit") Error: unexpected symbol in: "InfoPkgSeed",pgfFile = pgf, clfFile = clf, coreMps=mps, transFile=trans, probeFile = prob, author = "Dhanjit", email = "dasd at nirrh.res.in",biocViews = "AnnotationData",organism = "Marmoset", species = "Callithrix jacchus") makePdInfoPackage" > > seed <- new("AffyGenePDInfoPkgSeed", + pgfFile = pgf, clfFile = clf, coreMps=mps, transFile=trans, + probeFile = prob, author = "Dhanjit", + email = "dasd at nirrh.res.in", + biocViews = "AnnotationData", + organism = "Marmoset", species = "Callithrix jacchus") Error in getClass(Class, where = topenv(parent.frame())) : “AffyGenePDInfoPkgSeed” is not a defined class Thanks Dhanjit On Mon, Oct 28, 2013 at 7:20 PM, James W. MacDonald wrote: > You should be using either the oligo or xps package for this array. For > oligo, you need the pdInfoBuilder package, and some files from Affymetrix. > > You need the pgf, clf and mps files that are in this zipfile: > > http://www.affymetrix.com/**Auth/analysis/downloads/lf/wt/** > MarGene-1_0-st_rev01/MarGene-**1_0-st_rev01.zip > > And you need the probeset csv file > > http://www.affymetrix.com/**Auth/analysis/downloads/na33/** > wtgene-32_2/MarGene-1_0-st-v1.**na33.2.caljac3.probeset.csv.**zip > > and the transcript csv file > > http://www.affymetrix.com/**Auth/analysis/downloads/na33/** > wtgene-32_2/MarGene-1_0-st-v1.**na33.2.caljac3.transcript.csv.**zip > > and then you can make the pd.margene.1.0.st.v1 package following these > instructions: > > https://stat.ethz.ch/**pipermail/bioconductor/2013-**March/051335.html > > after which you can install using > > install.packages("pd.margene.**1.0.st.v1/", repos=NULL, type="source") > > If you want to use xps there are a set of vignettes here: > > http://www.bioconductor.org/**packages/release/bioc/html/**xps.html > > and Christian Stratowa is very helpful, so you can ask questions here if > you get stuck. > > Best, > > Jim > > > > > > On Monday, October 28, 2013 6:12:15 AM, DR DHANJIT KUMAR DAS [guest] wrote: > >> >> I would like to analyze data using Marmoset Gene 1.0 ST Array. While >> reading the CEL file into R environment, error message is showing as >> "Library - package margene10stcdf not installed" >> >> How to install the package MarGene-1_0st package into R environment? The >> R script is attached for your reference. >> >> The part No of the array is 901961. >> >> -- output of sessionInfo(): >> >> library(affy) >>> eset.rma <- justRMA(celfile.path="C:/**Dhanjit/Marmoset-Dr Uddhav/CEL >>> FILE/") >>> >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain MarGene-1_0-st >> Library - package margene10stcdf not installed >> Bioconductor - margene10stcdf not available >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > -- ** *---------------------------------------------------------------* *DR DHANJIT KUMAR DAS* Scientist C Genetic Research Centre National Institute for Research in Reproductive Health JM Street, Parel Mumbai - 400 012 Phone: 022-24192109 / 2145 Fax: 022-24147843 [[alternative HTML version deleted]]