Installing library package (Marmoset Gene 1.0 ST Array) into R environment
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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.
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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 at 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
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Dear James, Thank you so much for your reply. However, I would like to ask for R script (in sequence wise) to install MarGene 1.0st array library files into R environment. Kindly mention the R script for installation of MarGene 1.0st library files Thanks Dhanjit On Mon, Oct 28, 2013 at 7:20 PM, James W. MacDonald <jmacdon@uw.edu> 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<http: www.affymetri="" x.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<ht tp:="" 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< 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.ht ml<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< 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<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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]]
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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 <jmacdon@uw.edu> 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<http: www.affymetri="" x.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<ht tp:="" 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< 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.ht ml<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< 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<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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]]
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Hi Dhanjit, You need to both install and load the pdInfoBuilder package. So you need something like library(BiocInstaller) biocLite("pdInfoBuilder") library(pdInfoBuilder) And then you can proceed. You should also consider BiocUpgrade() to update your installation. Best, Jim On Tuesday, October 29, 2013 4:20:05 AM, Dhanjit K Das wrote: > 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 > <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 > <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 > <http: 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 > <http: 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 > <http: 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 <http: 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 <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> 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 > <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 > <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 > <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 > <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 <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 > <http: bioconductor.org="">. > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi James, Thank you so much for prompt reply. I could able to do that. However, making the PDInfoPacakage, I am getting error message as "Parsing file: coreMps... Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'coreMps': No such file or directory". Kindly suggest how to go about this problem I am sending the R script for your reference Thank you Dhanjit Output > mps <- list.files(baseDir, pattern = "MarGene-1_0-st.mps$", full.names = TRUE) > makePdInfoPackage(seed, destDir = ".") ====================================================================== =============================================================== Building annotation package for Affymetrix Gene ST Array PGF.........: MarGene-1_0-st.pgf CLF.........: MarGene-1_0-st.clf Probeset....: MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv Transcript..: MarGene-1_0-st-v1.na33.2.caljac3.transcript.csv Core MPS....: coreMps ====================================================================== =============================================================== Parsing file: MarGene-1_0-st.pgf... OK Parsing file: MarGene-1_0-st.clf... OK Creating initial table for probes... OK Creating dictionaries... OK Parsing file: MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv... OK Parsing file: coreMps... Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'coreMps': No such file or directory On Tue, Oct 29, 2013 at 6:36 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Dhanjit, > > You need to both install and load the pdInfoBuilder package. So you need > something like > > library(BiocInstaller) > biocLite("pdInfoBuilder") > library(pdInfoBuilder) > > And then you can proceed. > > You should also consider > > BiocUpgrade() > > to update your installation. > > Best, > > Jim > > > > > On Tuesday, October 29, 2013 4:20:05 AM, Dhanjit K Das wrote: > >> 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.h tml<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<http: bioconductor.o="" rg="" bioclite.r=""> >> <http: bioconductor.org="" **bioclite.r<http:="" bioconductor.org="" biocl="" ite.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<http: bioc="" onductor.org="" bioclite.r=""> >> <http: bioconductor.org="" **bioclite.r<http:="" bioconductor.org="" biocl="" ite.r="">>': >> Invalid argument >> >> > source("http://bioconductor.**org/biocLite.R<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 >> <http: 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 >> <http: 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 >> <http: 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 <http: 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 <jmacdon@uw.edu>> <mailto:jmacdon@uw.edu>> 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<http: www.affy="" metrix.com="" __auth="" analysis="" downloads="" lf="" wt="" __margene-1_0-st_rev01="" margene-__1_0-st_rev01.zip=""> >> >> <http: www.affymetrix.com="" **auth="" analysis="" downloads="" lf="" wt="" **="">> MarGene-1_0-st_rev01/MarGene-**1_0-st_rev01.zip<http: www.affymetr="" ix.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<http: www.affymetrix.com="" __auth="" analysis="" downloads="" na33="" __wtgene-="" 32_2="" margene-1_0-st-v1.__na33.2.caljac3.probeset.csv.__zip=""> >> >> <http: www.affymetrix.com="" **auth="" analysis="" downloads="" na33="" **="">> wtgene-32_2/MarGene-1_0-st-v1.**na33.2.caljac3.probeset.csv.**zip<h ttp:="" 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<http: www.affymetrix.com="" __auth="" analysis="" downloads="" na33="" __wtgene-32_2="" margene-="" 1_0-st-v1.__na33.2.caljac3.transcript.csv.__zip=""> >> >> <http: www.affymetrix.com="" **auth="" analysis="" downloads="" na33="" **="">> wtgene-32_2/MarGene-1_0-st-v1.**na33.2.caljac3.transcript.csv.**zip <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<https: stat.ethz.ch="" __pipermail="" bioconductor="" 201="" 3-__march="" 051335.html=""> >> >> <https: stat.ethz.ch="" **pipermail="" bioconductor="" 2013-**="">> March/051335.html<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<http: www.bioconductor.org="" __packages="" release="" bioc="" html="" _="" _xps.html="">< >> http://www.bioconductor.org/**packages/release/bioc/html/**xps.html <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 >> <http: bioconductor.org="">. >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<http s:="" stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https="" :="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__**science.biology.informatics.__** >> conductor<http: news.gmane.org="" gmane.__science.biology.informatics="" .__conductor=""> >> >> <http: news.gmane.org="" gmane.**science.biology.informatics.**="">> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> > >> >> >> -- >> 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 >> > > -- > 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]]
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Hi Dhanjit, On Tuesday, October 29, 2013 9:18:01 AM, Dhanjit K Das wrote: > Hi James, > > Thank you so much for prompt reply. I could able to do that. However, > making the PDInfoPacakage, I am getting error message as "Parsing > file: coreMps... Error in file(file, "rt") : cannot open the > connection In addition: Warning message: In file(file, "rt") : cannot > open file 'coreMps': No such file or directory". > > Kindly suggest how to go about this problem > > I am sending the R script for your reference > > Thank you > > Dhanjit > > Output > > > mps <- list.files(baseDir, pattern = "MarGene-1_0-st.mps$", > full.names = TRUE) > > makePdInfoPackage(seed, destDir = ".") > ==================================================================== ================================================================= > Building annotation package for Affymetrix Gene ST Array > PGF.........: MarGene-1_0-st.pgf > CLF.........: MarGene-1_0-st.clf > Probeset....: MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv > Transcript..: MarGene-1_0-st-v1.na33.2.caljac3.transcript.csv > Core MPS....: coreMps You need to do a better job of paying attention to the messages that are being given to you. Note that each of these things above are pointing to a real file, except for Core MPS, which says it is going to read in a file called 'coreMps'. Do you have any files called coreMps? > ==================================================================== ================================================================= > Parsing file: MarGene-1_0-st.pgf... OK > Parsing file: MarGene-1_0-st.clf... OK > Creating initial table for probes... OK > Creating dictionaries... OK > Parsing file: MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv... OK > Parsing file: coreMps... Error in file(file, "rt") : cannot open the > connection > In addition: Warning message: > In file(file, "rt") : cannot open file 'coreMps': No such file or > directory And here you are clearly being told that there is no such file called coreMps. I understand that this is new territory for you, but you have to take some initiative yourself to try and figure out why things aren't working as you expect. If you ever expect to get proficient with R and Bioconductor, you have to be able to self-diagnose problems, and this is a very simple thing to diagnose. Here is how to think about this: The function you are using is expecting some file that it is calling Core MPS, but is failing because it says there is no such file. Rather than asking for help, you could have looked back on the link I sent earlier: https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html to see what this Core MPS file should look like, and then look to see if you have something similar. This would have taken maybe two minutes and you would be on your way. You should think of the help you get on this list as being a limited resource. It is there for you to use, but only when you have exhausted your own ability to figure things out. Best, Jim > > > On Tue, Oct 29, 2013 at 6:36 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Dhanjit, > > You need to both install and load the pdInfoBuilder package. So > you need something like > > library(BiocInstaller) > biocLite("pdInfoBuilder") > library(pdInfoBuilder) > > And then you can proceed. > > You should also consider > > BiocUpgrade() > > to update your installation. > > Best, > > Jim > > > > > On Tuesday, October 29, 2013 4:20:05 AM, Dhanjit K Das wrote: > > 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 > <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 > <http: bioconductor.org="" bioclite.r=""> > <http: bioconductor.org="" __bioclite.r=""> <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 > <http: bioconductor.org="" bioclite.r=""> > <http: bioconductor.org="" __bioclite.r=""> <http: bioconductor.org="" bioclite.r="">>': Invalid argument > > > source("http://bioconductor.__org/biocLite.R > <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 <http: nirrh.res.in=""> > <http: 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 <http: nirrh.res.in=""> > <http: 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 <http: nirrh.res.in=""> > <http: 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 > <http: nirrh.res.in=""> <http: 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 > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> > <mailto:jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">>> 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 > <http: www.affymetrix.com="" __auth="" analysis="" downloads="" lf="" wt="" __margene-1_0-st_rev01="" margene-__1_0-st_rev01.zip=""> > > > <http: www.affymetrix.com="" __auth="" analysis="" downloads="" lf="" wt="" __margene-1_0-st_rev01="" margene-__1_0-st_rev01.zip=""> <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 > <http: www.affymetrix.com="" __auth="" analysis="" downloads="" na33="" __wtgene-32_2="" margene-1_0-st-v1.__na33.2.caljac3.probeset.csv.__zip=""> > > > <http: www.affymetrix.com="" __auth="" analysis="" downloads="" na33="" __wtgene-32_2="" margene-1_0-st-v1.__na33.2.caljac3.probeset.csv.__zip=""> <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 > <http: www.affymetrix.com="" __auth="" analysis="" downloads="" na33="" __wtgene-32_2="" margene-="" 1_0-st-v1.__na33.2.caljac3.transcript.csv.__zip=""> > > > <http: www.affymetrix.com="" __auth="" analysis="" downloads="" na33="" __wtgene-32_2="" margene-1_0-st-v1.__na33.2.caljac3.transcript.csv.__zip=""> <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-____Mar ch/051335.html > <https: stat.ethz.ch="" __pipermail="" bioconductor="" 2013-__march="" 051335.html=""> > > > <https: stat.ethz.ch="" __pipermail="" bioconductor="" 2013-__march="" 051335.html=""> <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 > <http: www.bioconductor.org="" __packages="" release="" bioc="" html="" __xps.html=""> > <http: www.bioconductor.org="" __packages="" release="" bioc="" html="" __xps.html=""> <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 <http: bioconductor.org=""> > <http: bioconductor.org="">. > > ___________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-__project.org=""> <mailto:bioconductor at="" r-project.org="">> > https://stat.ethz.ch/mailman/____listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> > > <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">> > Search the archives: > http://news.gmane.org/gmane.____science.biology.informatics. ____conductor > <http: news.gmane.org="" gmane.__science.biology.informatics._="" _conductor=""> > > > <http: news.gmane.org="" gmane.__science.biology.informatics.__conductor=""> <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 > > > -- > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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