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

Adeline Simon adeline.simon at versailles.inra.fr
Thu Oct 8 16:34:31 CEST 2009

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    
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
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 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
Avenue Lucien Brétignières
BP 01
78850 Thiverval-Grignon
Tel : 33 (0)1 30 81 45 68

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