[BioC] installing xps
cstrato at aon.at
Sat Dec 13 00:48:18 CET 2008
Here is the example code and verbose output how to import the pgf and
latest Affymetrix annotation file for MoGene:
Welcome to xps version 1.2.2
an R wrapper for XPS - eXpression Profiling System
(c) Copyright 2001-2008 by Christian Stratowa
> libdir <- "/Volumes/GigaDrive/Affy/libraryfiles"
> anndir <- "/Volumes/GigaDrive/Affy/Annotation"
> scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
> scheme.mogene10stv1r3.na27 <-
Creating new file
<1102500> records imported...Finished
New dataset <MoGene-1_0-st-v1> is added to Content...
Number of transcripts is <35519>.
<35519> records read...Finished
<35519> records imported...Finished
Reading data from input file...
Number of probesets is <35557>.
Note: Number of annotated probesets <35519> is not equal to number of
<35557> records read...Finished
Sorting data for probeset_type and position...
Total number of controls is <6682>
Note: no data for probeset type: control->chip...
Filling trees with data for probeset type: normgene, rescue...
Filling trees with data for probeset type: control->bgp...
Filling trees with data for probeset type: control->affx...
<35474> probeset tree entries read...Finished
Number of control->affx probesets is <22>.
Filling trees with data for probeset type: main...
Filling trees with data for non-annotated probesets...
<906151> records imported...Finished
<35557> total transcript units imported.
Genome cell statistics:
Number of unit cells: minimum = 4, maximum = 6515
For more example code how to use the Affymetrix whole Gene arrays,
please have a look at scripts "script4xps.R" and "script4exon.R", which
are located in directory xps/examples.
For Windows specific comments see:
Lana Schaffer wrote:
> Now I need to make sure that I can use the pgf and clf files
> (not the CDF) for the CEL file import?
> -----Original Message-----
> From: cstrato [mailto:cstrato at aon.at]
> Sent: Friday, December 12, 2008 2:42 PM
> To: Lana Schaffer
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] installing xps
> Dear Lana
> This is the usual error message you get when you have installed the
> wrong root version, because it cannot find the correct version of
> You need to install "root_v5.18.00.win32.vc80.msi" which you can
> download from:
> Best regards
> Lana Schaffer wrote:
>> I was unable to locate libCore.dll.
>> Where is this file?
>> -----Original Message-----
>> From: cstrato [mailto:cstrato at aon.at]
>> Sent: Friday, December 12, 2008 1:03 PM
>> To: Lana Schaffer
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] installing xps
>> Dear Lana
>> This is the most common question of Windows users:
>> Since Bioconductor has compiled the Windows version of xps using root
>> 5.18.00 you need to install the binary of this version.
>> Please see also my introductory comments for Windows users:
>> Best regards
>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>> V.i.e.n.n.a A.u.s.t.r.i.a
>> e.m.a.i.l: cstrato at aon.at
>> Lana Schaffer wrote:
>>> I am trying to install xps and get an error message when loading:
>>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>> unable to load shared library
>>> LoadLibrary failure: The specified procedure could not be found.
>>> Error: package/namespace load failed for 'xps'
>>> I have installed ROOT 5.19.02 from binary.
>>> Does this mean that I need to install ROOT from source?
>>> R version 2.8.0 (2008-10-20)
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>> attached base packages:
>>>  stats graphics grDevices utils datasets methods base
>>> loaded via a namespace (and not attached):
>>>  tools_2.8.0
>>> Lana Schaffer
>>> The Scripps Research Institute
>>> DNA Array Core Facility
>>> La Jolla, CA 92037
>>> (858) 784-2263
>>> (858) 784-2994
>>> schaffer at scripps.edu
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> Search the archives:
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