[BioC] installing xps

Sat Dec 13 00:48:18 CET 2008

Dear Lana

Here is the example code and verbose output how to import the pgf and 
latest Affymetrix annotation file for MoGene:

 > library(xps)

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 <- 
import.genome.scheme("Scheme_MoGene10stv1r3_na27",filedir=scmdir,
+                               
paste(libdir,"MoGene-1_0-st-v1.r3.analysis-lib-files/MoGene-1_0-st-v1.r3.clf",sep="/"),
+                               
paste(libdir,"MoGene-1_0-st-v1.r3.analysis-lib-files/MoGene-1_0-st-v1.r3.pgf",sep="/"),
+                               
paste(anndir,"Version08Nov/MoGene-1_0-st-v1.na27.mm9.transcript.csv",sep="/"))
Creating new file 
</Volumes/GigaDrive/CRAN/Workspaces/Schemes/Scheme_MoGene10stv1r3_na27.root>...
Importing 
</Volumes/GigaDrive/Affy/libraryfiles/MoGene-1_0-st-v1.r3.analysis-lib-files/MoGene-1_0-st-v1.r3.clf> 
as <MoGene-1_0-st-v1.cxy>...
   <1102500> records imported...Finished
New dataset <MoGene-1_0-st-v1> is added to Content...
Importing 
</Volumes/GigaDrive/Affy/Annotation/Version08Nov/MoGene-1_0-st-v1.na27.mm9.transcript.csv> 
as <MoGene-1_0-st-v1.ann>...
   Number of transcripts is <35519>.
   <35519> records read...Finished
   <35519> records imported...Finished
Importing 
</Volumes/GigaDrive/Affy/libraryfiles/MoGene-1_0-st-v1.r3.analysis-lib-files/MoGene-1_0-st-v1.r3.pgf> 
as <MoGene-1_0-st-v1.scm>...
   Reading data from input file...
   Number of probesets is <35557>.
Note: Number of annotated probesets <35519> is not equal to number of 
probesets <35557>.
   <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:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025452.html 

Best regards
Christian

Lana Schaffer wrote:
> Christian,
> Now I need to make sure that I can use the pgf and clf files
> (not the CDF) for the CEL file import?
> Lana 
>
> -----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
> libCore.dll.
>
> You need to install "root_v5.18.00.win32.vc80.msi" which you can
> download from:
> http://root.cern.ch/root/Version518.html
>
> Best regards
> Christian
>
> Lana Schaffer wrote:
>   
>> Christian,
>> I was unable to locate libCore.dll.
>> Where is this file?
>> Lana
>>
>> -----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:
>> https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025
>> 45
>> 2.html
>>
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> 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:
>>   
>>     
>>> Hi,
>>> 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
>>> 'C:/PROGRA~1/R/R-28~1.0/library/xps/libs/xps.dll':
>>>   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?
>>>
>>>   
>>>     
>>>       
>>>> sessionInfo()
>>>>     
>>>>       
>>>>         
>>> R version 2.8.0 (2008-10-20)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.8.0
>>>
>>> Lana Schaffer
>>> Biostatistics/Informatics
>>> 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
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>
>>>
>>>   
>>>     
>>>       
>>
>>   
>>     
>
>
>
>