[BioC] pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R

Benilton Carvalho bcarvalh at jhsph.edu
Thu Oct 8 17:24:30 CEST 2009

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- 
> 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
>>> _______________________________________________
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>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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> --
> Adeline SIMON
> Analyse Fonctionnelle du Génome de Botrytis cinerea
> INRA-AgroParisTech
> Avenue Lucien Brétignières
> BP 01
> 78850 Thiverval-Grignon
> Tel : 33 (0)1 30 81 45 68

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