[BioC] Installing library package (Marmoset Gene 1.0 ST Array) into R environment
James W. MacDonald
jmacdon at uw.edu
Tue Oct 29 14:35:33 CET 2013
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-____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>
> <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
>
>
>
>
> --
> /**/
> /*---------------------------------------------------------------*/
> /*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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