[BioC] Installing library package (Marmoset Gene 1.0 ST Array) into R environment
James W. MacDonald
jmacdon at uw.edu
Tue Oct 29 14:06:25 CET 2013
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>.
>
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>
> --
> 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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