[BioC] pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R
Adeline Simon
adeline.simon at versailles.inra.fr
Fri Oct 9 16:09:23 CEST 2009
Thanks, Jim
I found the necessary documentation.
Adeline
James W. MacDonald a écrit :
> 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/inst/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 compressé
>> '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 écrit :
>>> 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 écrit :
>>>>>> 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 Génome de Botrytis cinerea
>>>>> INRA-AgroParisTech
>>>>> UMR1290 BIOGER-CPP
>>>>> Avenue Lucien Brétignières
>>>>> BP 01
>>>>> 78850 Thiverval-Grignon
>>>>> Tel : 33 (0)1 30 81 45 68
>>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
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>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>
>
--
Adeline SIMON
Analyse Fonctionnelle du Génome de Botrytis cinerea
INRA-AgroParisTech
UMR1290 BIOGER-CPP
Avenue Lucien Brétignières
BP 01
78850 Thiverval-Grignon
Tel : 33 (0)1 30 81 45 68
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