[BioC] pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R
Benilton Carvalho
bcarvalh at jhsph.edu
Fri Oct 9 16:10:12 CEST 2009
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/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
>>> 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
>
More information about the Bioconductor
mailing list