[BioC] pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R
adeline.simon at versailles.inra.fr
Fri Oct 9 14:18:46 CEST 2009
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:
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
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
Sorry for the error message partly in French...
Benilton Carvalho a écrit :
> 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,
> 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):
>> 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")
>> ## 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,
>> 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,
>> 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-
>>> expression). For each of these projects, Nimblegen provided pair and
>>> calls files (raw and normalized) and design files: ndf and ngd, and
>>> documentation, but they have never sent xys file in the CD. I think
>>> 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 :
>>>> 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
>>> 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
>>> 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,
>>> 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
>>>> sessionInfo(). Regarding the XYS files, these are produced by
>>>> NimbleScan (AFAIK) and are well described in NimbleGen documentation.
>>>> On Oct 8, 2009, at 9:24 AM, "Adeline Simon"
>>>> <adeline.simon at versailles.inra.fr
>>>>> 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.
>>>>> Adeline SIMON
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> Search the archives:
>>> Adeline SIMON
>>> Analyse Fonctionnelle du Génome de Botrytis cinerea
>>> UMR1290 BIOGER-CPP
>>> Avenue Lucien Brétignières
>>> BP 01
>>> 78850 Thiverval-Grignon
>>> Tel : 33 (0)1 30 81 45 68
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