[BioC] XPS: Human Gene 1.0 ST v1 Summarization using Affy Library r4
Luis Campos
lfcampos at ucdavis.edu
Thu Apr 22 00:00:40 CEST 2010
Dear Christian,
I managed to create the ROOT file using the files you indicated and my
output now matches exactly with yours using the Rterm. Thank you very
much for your help and quick response.
~Luis Campos
Luis Campos
Junior Specialist
Division of Biostatistics
Public Health Sciences, UC Davis
530-752-4046
On 4/21/2010 2:29 PM, cstrato wrote:
> 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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