[BioC] pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R
adeline.simon at versailles.inra.fr
Thu Oct 8 16:34:31 CEST 2009
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 :
> 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
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 your
> 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
> > 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.
>> Adeline SIMON
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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