Thanks, Jim I found the necessary documentation. Adeline James W. MacDonald a ?crit : > Hi Adeline, > > You should look here: > > > http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I -install-packages-into-libraries-in-this-version_003f > > > Best, > > Jim > > > > Adeline Simon wrote: >> Thanks, Benilton, for these comprehensive explanation. >> I actually did not understand the need to build a package before >> using the function read.xysfiles. >> >> I well managed to read xys files as in the example given in the page: >> http://www.bioconductor.org/packages/release/bioc/vignettes/oligo/i nst/doc/oligoNimblegenExpression.pdf >> >> That is OK >> However, to test the package on my data, I have to get valid XYS >> files from Nimblegen (I thought I could build them from pair files, >> but it is not possible since pair files don't contain the >> NGS_CONTROLS, V_CODE and H_CODE results). >> Nevertheless, using your example XYS and ndf files, I was able to >> re-create an annotation package with the commands you detailed, but >> not to install it with the install.packages command (R-2.9.2 on >> Windows). >> But the problem doesn't seem to be specific to the packages created >> by Oligo package. When I will have R-2.9.2 installed on unix, I think >> the R CMD buid and R CMD INSTALL will function. >> >> >> > install.packages("pd.essai.60mer.expr.tar.gz", repos=NULL) >> Erreur dans gzfile(file, "r") : impossible d'ouvrir la connexion >> De plus : Warning messages: >> 1: In unzip(zipname, exdir = dest) : >> erreur 1 lors de l'extraction d'un fichier zip >> 2: In gzfile(file, "r") : >> impossible d'ouvrir le fichier compress? >> 'pd.essai.60mer.expr.tar.gz/DESCRIPTION', cause probable : 'No such >> file or directory' >> >> Sorry for the error message partly in French... >> >> >> >> Thanks again. >> Best whishes, >> Adeline >> >> >> Benilton Carvalho a ?crit : >>> Adeline, >>> >>> it was just brought to my attention that I forgot to mention that >>> the very last step (installation of the annotation package you just >>> created) can be done from within R. >>> >>> If you use: >>> >>> install.packages(PKGNAME, repos=NULL) >>> >>> the package will be installed without needing to use "R CMD build" >>> and "R CMD INSTALL". >>> >>> Apologies for missing that, >>> >>> b >>> >>> On Oct 8, 2009, at 12:24 PM, Benilton Carvalho wrote: >>> >>>> Dear Adeline, >>>> >>>> the problem you report is due to the fact you don't have the required >>>> annotation package installed. >>>> >>>> Because the example you downloaded is not an expression experiment, my >>>> suggestion is to use the one shown on the vignette (given that you >>>> didn't provide a sessionInfo(), I assume you're running R 2.9.2): >>>> >>>> http://www.bioconductor.org/packages/release/bioc/vignettes/oligo /inst/doc/oligoNimblegenExpression.pdf >>>> >>>> >>>> In order to run the analysis described on the aforementioned PDF, you >>>> will mainly need the following packages: >>>> >>>> - pd.hg18.60mer.expr >>>> - maqcExpression4plex >>>> >>>> pd.hg18.60mer.expr is the annotation package needed to read in the XYS >>>> files (produced by NimbleGen) provided by maqcExpression4plex. The "pd >>>> package", as described by the vignette, was built using the >>>> pdInfoBuilder package. >>>> >>>> So, to run the vignette example, my suggestion is (under R 2.9.2 and >>>> the latest BioC): >>>> >>>> ## start >>>> pkgs = c("oligo", "pd.hg18.60mer.expr", "maqcExpression4plex", >>>> "genefilter", "limma", "RColorBrewer") >>>> source("http://www.bioconductor.org/biocLite.R") >>>> biocLite(pkgs) >>>> ## end >>>> >>>> Once the packages are installed, you will be able to run that >>>> particular example. >>>> >>>> When working with your own experiment, you will need to create the >>>> annotation package for your data. To do that, you will need to use the >>>> pdInfoBuilder package and you can use its vignette "Building >>>> Annotation Packages with pdInfoBuilder for Use with the oligo >>>> Package" (in particular, Section 9) as a reference. >>>> >>>> Anyways, to create your annotation package (for NimbleGen Expression), >>>> you will need: >>>> >>>> - NDF file >>>> - XYS file (one suffices, as it will be ued as templates) >>>> - pdInfoBuilder package >>>> >>>> Once everything is in place, you need (replace capital letters by the >>>> appropriate values): >>>> >>>> seed <- new("NgsExpressionPDInfoPkgSeed", >>>> ndfFile=YOURNDF, xysFile=YOURXYS, >>>> author=YOU, email=EMAIL, >>>> biocViews="AnnotationData", >>>> genomebuild=BUILD, organism=ORG, >>>> species=SP, url=URL) >>>> makePdInfoPackage(seed, destDir = ".") >>>> >>>> This will create the package under your current directory. After the >>>> package structure is created, you need to build and install it (using >>>> the regular R CMD build and R CMD INSTALL). >>>> >>>> Please let me know how this works for you, >>>> >>>> With best wishes, >>>> >>>> b >>>> >>>> On Oct 8, 2009, at 11:34 AM, Adeline Simon wrote: >>>> >>>>> Dear Benilton, >>>>> >>>>> I'm pleased that you answered, you will probably have a solution... >>>>> >>>>> As I wrote, the problem is the same than Jean-Yves Sgro posted, >>>>> that's >>>>> why I didn't detailed. >>>>> But, you are right, it's better to detail. >>>>> >>>>> I manage several projects that contain data sent by Nimblegen (one- >>>>> color >>>>> expression). For each of these projects, Nimblegen provided pair and >>>>> calls files (raw and normalized) and design files: ndf and ngd, and >>>>> some >>>>> documentation, but they have never sent xys file in the CD. I think >>>>> we >>>>> can get them on request ; indeed, as you mentionned, these files are >>>>> documented, but I confirm that Nimblegen do not routinely send them. >>>>> >>>>> Nevertheless, I downloaded examples of XYS files from web (Rafael >>>>> Irizzary web page : http://rafalab.jhsph.edu/software.html) : human >>>>> samples (296MB), and tried to create a FeatureSet object. >>>>> >>>>> I placed the xys files in the current directory and performed : >>>>>> libray(oligo) >>>>>> xysobj = read.xysfiles(list.xysfiles()) >>>>> Loading required package: pd.feinberg.mm8.me.hx1 >>>>> Erreur dans read.xysfiles(list.xysfiles()) : >>>>> Must install the pd.feinberg.mm8.me.hx1 package. >>>>> De plus : Warning message: >>>>> In library(package, lib.loc = lib.loc, character.only = TRUE, >>>>> logical.return = TRUE, : >>>>> there is no package called 'pd.feinberg.mm8.me.hx1' >>>>> >>>>> >>>>> >>>>> feinberg.mm8.me.hx1 is the design name >>>>> >>>>> I also tried with my data I formated to create xys files, and the >>>>> message was the same (replacing feinberg.mm8.me.hx1by my design name) >>>>> >>>>> In the documentation, only xys files are mandatory to use the >>>>> function. >>>>> The xys files I use seem to be well formated : (see below the first 5 >>>>> lines of a xys file from Rafael Irizarry) : >>>>> >>>>> # software=NimbleScan version=2.4.29 >>>>> imagefile=/nfs/oldimages/Not_in_NOSS/2008/07_july/04_Hopkins/ >>>>> NG096_20080731/273592_635.tif >>>>> designfile=/nfs/bioinfo/designs/Feinberg_MM8_Me_HX1.ndf >>>>> designname=Feinberg_MM8_Me_HX1 designid=6356 date=Fri Aug 01 >>>>> 08:13:59 GMT 2008 border=0 ul_x=156.682 ul_y=89.519 >>>>> ur_x=3018.304 ur_y=72.633 lr_x=3038.485 lr_y=3890.945 >>>>> ll_x=176.468 ll_y=3907.360 score=0.241 qcscore=0.211 >>>>> locallyaligned=no correctAstig=no Knots= auto=no >>>>> X Y SIGNAL COUNT >>>>> 1 1 246.89 1 >>>>> 23 1 11997.00 1 >>>>> 25 1 230.00 1 >>>>> >>>>> >>>>> I hope you will see a solution, >>>>> Thanks, >>>>> >>>>> Adeline >>>>> >>>>> >>>>> >>>>> >>>>> Carvalho, Benilton a ?crit : >>>>>> Dear Adeline, >>>>>> >>>>>> I'd appreciate if you could provide detailed information about what >>>>>> the problemis (or the link to the report you refer to) along with >>>>>> your >>>>>> sessionInfo(). Regarding the XYS files, these are produced by >>>>>> NimbleScan (AFAIK) and are well described in NimbleGen >>>>>> documentation. >>>>>> >>>>>> Cheers, >>>>>> >>>>>> b >>>>>> >>>>>> On Oct 8, 2009, at 9:24 AM, "Adeline Simon" >>>>>> <adeline.simon at="" versailles.inra.fr="">>>>>>> wrote: >>>>>> >>>>>> >>>>>>> October 2009. >>>>>>> >>>>>>> I have exactly the same problem Jean-Yves Sgro, posted on July >>>>>>> 2008. >>>>>>> I don't succeed in using the read.xysfiles function of oligo >>>>>>> package !!? >>>>>>> (same error messages) >>>>>>> Furthermore, as Nimblegen doesn't provide XYS files by default, I'm >>>>>>> especially interested to know if there are packages for Nimblegen >>>>>>> analyses without the XYS files, but rather using the .pair or other >>>>>>> standard files really provided by Nimblegen. >>>>>>> Thanks, >>>>>>> >>>>>>> Adeline SIMON >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>> >>>>> >>>>> -- >>>>> Adeline SIMON >>>>> Analyse Fonctionnelle du G?nome de Botrytis cinerea >>>>> INRA-AgroParisTech >>>>> UMR1290 BIOGER-CPP >>>>> Avenue Lucien Br?tigni?res >>>>> BP 01 >>>>> 78850 Thiverval-Grignon >>>>> Tel : 33 (0)1 30 81 45 68 >>>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > -- Adeline SIMON Analyse Fonctionnelle du G?nome de Botrytis cinerea INRA-AgroParisTech UMR1290 BIOGER-CPP Avenue Lucien Br?tigni?res BP 01 78850 Thiverval-Grignon Tel : 33 (0)1 30 81 45 68

Hi, Benilton, I finally installed R 2.9.2 on unix, and everything is OK. Thanks, Adeline Benilton Carvalho a ?crit : > Hi Adeline, > > If I were to run the makePdInfoPackage() function with your data, I'd > get something like (I can't remember precisely the message): > > "pd.essai.60mer.expr package created" > > So, on my machine (UNIX-based), it suffices to type, in R: > > install.packages("pd.essai.60mer.exp", repos=NULL) > > But I don't have a Windows machine to test wether or not this is valid > on Windows.... If it doesn't, one (proper) way of getting a zip file > is uploading the .tar.gz to: > > http://win-builder.r-project.org/ > > Never tried that myself, but I was told that because there isn't > compilation involved with packages like this, you may create a zip > file of the directory 'pd.essai.60mer.expr' and install it on Windows > using the "Install From Local Zip" option available on Rgui... But, > again, I had never done that... > > b > > On Oct 9, 2009, at 9:18 AM, Adeline Simon wrote: > >> Thanks, Benilton, for these comprehensive explanation. >> I actually did not understand the need to build a package before using >> the function read.xysfiles. >> >> I well managed to read xys files as in the example given in the page: >> http://www.bioconductor.org/packages/release/bioc/vignettes/oligo/i nst/doc/oligoNimblegenExpression.pdf >> >> >> That is OK >> However, to test the package on my data, I have to get valid XYS files >> from Nimblegen (I thought I could build them from pair files, but it is >> not possible since pair files don't contain the NGS_CONTROLS, V_CODE and >> H_CODE results). >> Nevertheless, using your example XYS and ndf files, I was able to >> re-create an annotation package with the commands you detailed, but not >> to install it with the install.packages command (R-2.9.2 on Windows). >> But the problem doesn't seem to be specific to the packages created by >> Oligo package. When I will have R-2.9.2 installed on unix, I think the R >> CMD buid and R CMD INSTALL will function. >> >> >>> install.packages("pd.essai.60mer.expr.tar.gz", repos=NULL) >> Erreur dans gzfile(file, "r") : impossible d'ouvrir la connexion >> De plus : Warning messages: >> 1: In unzip(zipname, exdir = dest) : >> erreur 1 lors de l'extraction d'un fichier zip >> 2: In gzfile(file, "r") : >> impossible d'ouvrir le fichier compress? >> 'pd.essai.60mer.expr.tar.gz/DESCRIPTION', cause probable : 'No such file >> or directory' >> >> Sorry for the error message partly in French... >> >> >> >> Thanks again. >> Best whishes, >> Adeline >> >> >> Benilton Carvalho a ?crit : >>> Adeline, >>> >>> it was just brought to my attention that I forgot to mention that the >>> very last step (installation of the annotation package you just >>> created) can be done from within R. >>> >>> If you use: >>> >>> install.packages(PKGNAME, repos=NULL) >>> >>> the package will be installed without needing to use "R CMD build" and >>> "R CMD INSTALL". >>> >>> Apologies for missing that, >>> >>> b >>> >>> On Oct 8, 2009, at 12:24 PM, Benilton Carvalho wrote: >>> >>>> Dear Adeline, >>>> >>>> the problem you report is due to the fact you don't have the required >>>> annotation package installed. >>>> >>>> Because the example you downloaded is not an expression experiment, my >>>> suggestion is to use the one shown on the vignette (given that you >>>> didn't provide a sessionInfo(), I assume you're running R 2.9.2): >>>> >>>> http://www.bioconductor.org/packages/release/bioc/vignettes/oligo /inst/doc/oligoNimblegenExpression.pdf >>>> >>>> >>>> >>>> In order to run the analysis described on the aforementioned PDF, you >>>> will mainly need the following packages: >>>> >>>> - pd.hg18.60mer.expr >>>> - maqcExpression4plex >>>> >>>> pd.hg18.60mer.expr is the annotation package needed to read in the XYS >>>> files (produced by NimbleGen) provided by maqcExpression4plex. The "pd >>>> package", as described by the vignette, was built using the >>>> pdInfoBuilder package. >>>> >>>> So, to run the vignette example, my suggestion is (under R 2.9.2 and >>>> the latest BioC): >>>> >>>> ## start >>>> pkgs = c("oligo", "pd.hg18.60mer.expr", "maqcExpression4plex", >>>> "genefilter", "limma", "RColorBrewer") >>>> source("http://www.bioconductor.org/biocLite.R") >>>> biocLite(pkgs) >>>> ## end >>>> >>>> Once the packages are installed, you will be able to run that >>>> particular example. >>>> >>>> When working with your own experiment, you will need to create the >>>> annotation package for your data. To do that, you will need to use the >>>> pdInfoBuilder package and you can use its vignette "Building >>>> Annotation Packages with pdInfoBuilder for Use with the oligo >>>> Package" (in particular, Section 9) as a reference. >>>> >>>> Anyways, to create your annotation package (for NimbleGen Expression), >>>> you will need: >>>> >>>> - NDF file >>>> - XYS file (one suffices, as it will be ued as templates) >>>> - pdInfoBuilder package >>>> >>>> Once everything is in place, you need (replace capital letters by the >>>> appropriate values): >>>> >>>> seed <- new("NgsExpressionPDInfoPkgSeed", >>>> ndfFile=YOURNDF, xysFile=YOURXYS, >>>> author=YOU, email=EMAIL, >>>> biocViews="AnnotationData", >>>> genomebuild=BUILD, organism=ORG, >>>> species=SP, url=URL) >>>> makePdInfoPackage(seed, destDir = ".") >>>> >>>> This will create the package under your current directory. After the >>>> package structure is created, you need to build and install it (using >>>> the regular R CMD build and R CMD INSTALL). >>>> >>>> Please let me know how this works for you, >>>> >>>> With best wishes, >>>> >>>> b >>>> >>>> On Oct 8, 2009, at 11:34 AM, Adeline Simon wrote: >>>> >>>>> Dear Benilton, >>>>> >>>>> I'm pleased that you answered, you will probably have a solution... >>>>> >>>>> As I wrote, the problem is the same than Jean-Yves Sgro posted, >>>>> that's >>>>> why I didn't detailed. >>>>> But, you are right, it's better to detail. >>>>> >>>>> I manage several projects that contain data sent by Nimblegen (one- >>>>> color >>>>> expression). For each of these projects, Nimblegen provided pair and >>>>> calls files (raw and normalized) and design files: ndf and ngd, and >>>>> some >>>>> documentation, but they have never sent xys file in the CD. I think >>>>> we >>>>> can get them on request ; indeed, as you mentionned, these files are >>>>> documented, but I confirm that Nimblegen do not routinely send them. >>>>> >>>>> Nevertheless, I downloaded examples of XYS files from web (Rafael >>>>> Irizzary web page : http://rafalab.jhsph.edu/software.html) : human >>>>> samples (296MB), and tried to create a FeatureSet object. >>>>> >>>>> I placed the xys files in the current directory and performed : >>>>>> libray(oligo) >>>>>> xysobj = read.xysfiles(list.xysfiles()) >>>>> Loading required package: pd.feinberg.mm8.me.hx1 >>>>> Erreur dans read.xysfiles(list.xysfiles()) : >>>>> Must install the pd.feinberg.mm8.me.hx1 package. >>>>> De plus : Warning message: >>>>> In library(package, lib.loc = lib.loc, character.only = TRUE, >>>>> logical.return = TRUE, : >>>>> there is no package called 'pd.feinberg.mm8.me.hx1' >>>>> >>>>> >>>>> >>>>> feinberg.mm8.me.hx1 is the design name >>>>> >>>>> I also tried with my data I formated to create xys files, and the >>>>> message was the same (replacing feinberg.mm8.me.hx1by my design name) >>>>> >>>>> In the documentation, only xys files are mandatory to use the >>>>> function. >>>>> The xys files I use seem to be well formated : (see below the first 5 >>>>> lines of a xys file from Rafael Irizarry) : >>>>> >>>>> # software=NimbleScan version=2.4.29 >>>>> imagefile=/nfs/oldimages/Not_in_NOSS/2008/07_july/04_Hopkins/ >>>>> NG096_20080731/273592_635.tif >>>>> designfile=/nfs/bioinfo/designs/Feinberg_MM8_Me_HX1.ndf >>>>> designname=Feinberg_MM8_Me_HX1 designid=6356 date=Fri Aug 01 >>>>> 08:13:59 GMT 2008 border=0 ul_x=156.682 ul_y=89.519 >>>>> ur_x=3018.304 ur_y=72.633 lr_x=3038.485 lr_y=3890.945 >>>>> ll_x=176.468 ll_y=3907.360 score=0.241 qcscore=0.211 >>>>> locallyaligned=no correctAstig=no Knots= auto=no >>>>> X Y SIGNAL COUNT >>>>> 1 1 246.89 1 >>>>> 23 1 11997.00 1 >>>>> 25 1 230.00 1 >>>>> >>>>> >>>>> I hope you will see a solution, >>>>> Thanks, >>>>> >>>>> Adeline >>>>> >>>>> >>>>> >>>>> >>>>> Carvalho, Benilton a ?crit : >>>>>> Dear Adeline, >>>>>> >>>>>> I'd appreciate if you could provide detailed information about what >>>>>> the problemis (or the link to the report you refer to) along with >>>>>> your >>>>>> sessionInfo(). Regarding the XYS files, these are produced by >>>>>> NimbleScan (AFAIK) and are well described in NimbleGen >>>>>> documentation. >>>>>> >>>>>> Cheers, >>>>>> >>>>>> b >>>>>> >>>>>> On Oct 8, 2009, at 9:24 AM, "Adeline Simon" >>>>>> <adeline.simon at="" versailles.inra.fr="">>>>>>> wrote: >>>>>> >>>>>> >>>>>>> October 2009. >>>>>>> >>>>>>> I have exactly the same problem Jean-Yves Sgro, posted on July >>>>>>> 2008. >>>>>>> I don't succeed in using the read.xysfiles function of oligo >>>>>>> package !!? >>>>>>> (same error messages) >>>>>>> Furthermore, as Nimblegen doesn't provide XYS files by default, I'm >>>>>>> especially interested to know if there are packages for Nimblegen >>>>>>> analyses without the XYS files, but rather using the .pair or other >>>>>>> standard files really provided by Nimblegen. >>>>>>> Thanks, >>>>>>> >>>>>>> Adeline SIMON >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>> >>>>> >>>>> -- >>>>> Adeline SIMON >>>>> Analyse Fonctionnelle du G?nome de Botrytis cinerea >>>>> INRA-AgroParisTech >>>>> UMR1290 BIOGER-CPP >>>>> Avenue Lucien Br?tigni?res >>>>> BP 01 >>>>> 78850 Thiverval-Grignon >>>>> Tel : 33 (0)1 30 81 45 68 >>>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> -- >> Adeline SIMON >> Analyse Fonctionnelle du G?nome de Botrytis cinerea >> INRA-AgroParisTech >> UMR1290 BIOGER-CPP >> Avenue Lucien Br?tigni?res >> BP 01 >> 78850 Thiverval-Grignon >> Tel : 33 (0)1 30 81 45 68 >> > -- Adeline SIMON Analyse Fonctionnelle du G?nome de Botrytis cinerea INRA-AgroParisTech UMR1290 BIOGER-CPP Avenue Lucien Br?tigni?res BP 01 78850 Thiverval-Grignon Tel : 33 (0)1 30 81 45 68