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.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>",**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.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-__**
>> March/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>.
>>
>>         ______________________________**___________________
>>         Bioconductor mailing list
>>         Bioconductor@r-project.org <mailto:Bioconductor@r-**project.org<Bioconductor@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

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