[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):
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
>>>
>>> _______________________________________________
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>>>
>
>
> --
> 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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