[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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