[BioC] XPS: Human Gene 1.0 ST v1 Summarization using Affy Library r4

cstrato cstrato at aon.at
Wed Apr 21 23:29:36 CEST 2010


Dear Luis,

I have just tested to create the scheme file for the HuGene array on 
Windows XP. Here is the output I get:

 > library(xps)

Welcome to xps version 1.6.4
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2009 by Christian Stratowa

 > libdir <- "C:/home/Rabbitus/Firma/Affy/libraryfiles"
 > anndir <- "C:/home/Rabbitus/Firma/Affy/Annotation"
 > scmdir <- "C:/home/Rabbitus/CRAN/workspaces/schemes"
 > scheme.hugene <- 
import.exon.scheme("Scheme_HuGene10stv1r4_na301_hg19",filedir=scmdir,
+                  paste(libdir,"HuGene-1_0-st-v1.r4.clf",sep="/"),
+                  paste(libdir,"HuGene-1_0-st-v1.r4.pgf",sep="/"),
+                  
paste(anndir,"HuGene-1_1-st-v1.na30.1.hg19.probeset.csv",sep="/")
+                  
paste(anndir,"HuGene-1_1-st-v1.na30.hg19.transcript.csv",sep="/"))
Creating new file 
<C:/home/Rabbitus/CRAN/workspaces/schemes/Scheme_HuGene10stv1r4_na301_hg19.roo
t>...
Importing 
<C:/home/Rabbitus/Firma/Affy/libraryfiles/HuGene-1_0-st-v1.r4.clf> as 
<HuGene-1_0-st-v1.cxy>...
   <1102500> records imported...Finished
New dataset <HuGene-1_0-st-v1> is added to Content...
Importing 
<C:/home/Rabbitus/Firma/Affy/Annotation/HuGene-1_1-st-v1.na30.1.hg19.probeset.csv> 
as <HuGene-1_0-st-v1.anp>...
   Number of probesets is <257022>.
   <257022> records read...Finished
   <256977> records imported...Finished
   <209826> exon annotations imported.
Importing 
<C:/home/Rabbitus/Firma/Affy/libraryfiles/HuGene-1_0-st-v1.r4.pgf> as 
<HuGene-1_0-st-v1.scm>...
   Reading data from input file...
   Number of probesets is <257430>.
   Note: Number of annotated probesets <257022> is not equal to number 
of probesets <257430>.
   <257430> records read...Finished
   Sorting data for probeset_type and position...
   Total number of controls is <45>
   Filling trees with data for probeset type: control->chip...
   Number of control->chip items is <0>.
   Filling trees with data for probeset type: control->bgp...
   Filling trees with data for probeset type: control->affx...
   Number of control->affx probesets is <57>.
   Filling trees with data for probeset type: main...
   <256977> probeset tree entries read...Finished
Note: Number of exons imported <209825> is not equal to number of 
annotated exons <209826>.
   Filling trees with data for non-annotated probesets...
   <861493> records imported...Finished
   <33665> total transcript units imported.
   <214661> total exon array units imported.
   Exon cell statistics:
      Number of probeset cells: minimum = 1,  maximum = 1189
      Number of exon cells:     minimum = 1,  maximum = 1189
      Number of unit cells:     minimum = 1,  maximum = 1189
Importing 
<C:/home/Rabbitus/Firma/Affy/Annotation/HuGene-1_1-st-v1.na30.hg19.transcript.csv> 
as
<HuGene-1_0-st-v1.ann>...
   Number of annotated transcripts is <33257>.
   <33257> records read...Finished
   <33212> records imported...Finished
 >

As I mentioned before, if you still get an error please send me the 
complete output.

Best regards
Christian


cstrato wrote:
> Dear Luis,
>
> The annotation file "HuGene-1_1-st-v1.na30.hg19.probeset.csv" contains 
> probesets which are not present in the pgf-file. For this reason 
> Affymetrix has updated the file to 
> "HuGene-1_1-st-v1.na30.1.hg19.probeset.csv". Could you please use this 
> annotation file.
> (Files "HuGene-1_1-st-v1.na30.hg19.transcript.csv" and 
> "HuGene-1_0-st-v1.na30.hg19.transcript.csv" should be identical.)
>
> If you still have problems could you please use Rterm with 
> verbose=TRUE and send me the complete output.
>
> 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
> _._._._._._._._._._._._._._._._._._
>
>
>
> Luis Campos wrote:
>> Hi,
>>
>> I have run into an error that I cannot quite figure out. I want to run a
>> summarization on the Human Gene 1.0 ST v1 chip using the XPS package and
>> using the 4th revision of the library (r4). I have looked through the
>> mailing list and cannot seem to find someone who had the same problem.
>>
>> Since r4 is now essentially an exon scheme i used import.exon.scheme as
>> mentioned in the help files as follows:
>>
>>  >  library(xps)
>> Welcome to xps version 1.6.4
>>      an R wrapper for XPS - eXpression Profiling System
>>      (c) Copyright 2001-2009 by Christian Stratowa
>>
>> *(it was suggested to use the entire directory when inserting the file
>> name as below)
>> *(since I m on a Windows XP machine, I have also tried: paste, "\\"
>> instead of "/")
>>  >  scheme.hugene10stv1r4.na30 = import.exon.scheme(filename   =
>> "HuGene_10_st_v1",
>>                     filedir    = "G:/APT/XPS",
>>                     layoutfile = 
>> "G:/APT/Affy_lib/HuGene-1_0-st-v1.r4.clf",
>>                     schemefile = 
>> "G:/APT/Affy_lib/HuGene-1_0-st-v1.r4.pgf",
>>                     probeset   =
>> "G:/APT/Affy_lib/HuGene-1_0-st-v1.na30.hg19.probeset.csv",
>>                     transcript =
>> "G:/APT/Affy_lib/HuGene-1_0-st-v1.na30.hg19.transcript.csv",
>>                     add.mask   = FALSE,
>>                     verbose    = TRUE)
>> I get the following Error:
>>      Error in import.exon.scheme(filename = "HuGene_10_st_v1", filedir =
>> "G:/APT/XPS",  :
>>    error in function 'ImportExonSchemes'
>>
>> (I checked the error value and it is (-13))
>>
>> ***It was mentioned in the help page for import.exon.scheme thata ",
>> since Affymetrix is still changing the headers and/or columns of the
>> annotation files, future annotation files may require adaptation of the
>> source code, thus the current version of 'xps' may not be able to read
>> these files."***
>> If this is the case, since I have the most updated version of the
>> Annotation and library files, could this be the problem?
>>
>> Also, in the internal 'ImportExonSchemes' function the error that is
>> occuring has the non-zero value of -13, this may help.Thank you very
>> much in advance.
>>
>>
>> Here is my Session Info:
>>
>>>  sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252 
>> LC_CTYPE=English_UnitedStates.1252  [3] LC_MONETARY=English_United 
>> States.1252 LC_NUMERIC=C                         [5] 
>> LC_TIME=English_United States.1252  attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods  base   
>> other attached packages:
>> [1] xps_1.6.4
>>
>>
>>
>> ~Luis Campos
>>
>>
>
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