[BioC] pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R
bcarvalh at jhsph.edu
Thu Oct 8 17:39:41 CEST 2009
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:
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,
>> 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
>>> 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
>>>> 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: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 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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