[BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR

[cstrato]

Dear Endo,

I can reproduce the error you get. The reason is the following:

Since many years all the Affymetrix annotation files that I have tested 
(and that people have used) contain in their header files the 
information about the 'genome-species', e.g. line 5 for human arrays 
contains:
#%genome-species=Homo sapiens

For some reason Affymetrix has decided to delete this line in the 
Arabidopsis arrays (and maybe some other arrays).

Thus please open in an editor the probeset and the transcript annotation 
files and add as line 5 the following line:
#%genome-species=Arabidopsis

Then you will be able to create the scheme file w/o problems.

For the next release I will update the development version of xps so 
that it will report a warning instead of an error.

Best regards,
Christian


On 2/16/13 11:04 AM, Endo [guest] wrote:
>
> Hi,
>
> I have struggled with an error that I cannot quite figure out.
> I'm using 64-bit Mac OSX (10.7.5) and would like to analyze Arabidopsis Gene 1.0 ST chip data by using the XPS package.
>
> I used import.exon.scheme as mentioned in the help files as follows:
>
>> library(xps)
> Welcome to xps version 1.18.1
>      an R wrapper for XPS - eXpression Profiling System
>      (c) Copyright 2001-2012 by Christian Stratowa
>> libdir <- "~/desktop/workspace/libdir"
>> anndir <- "~/desktop/workspace/anndir"
>> scmdir <- "~/desktop/workspace/scmdir"
>> scheme.aragene10stv1.na33 <-
> + import.exon.scheme("Scheme_AraGene10stv1_na33", filedir = scmdir,
> +    paste(libdir, "AraGene-1_0-st.clf",sep="/"),
> +    paste(libdir, "AraGene-1_0-st.pgf",sep="/"),
> +    paste(anndir, "AraGene-1_0-st-v1.na33.tair10.probeset.csv",sep="/"),
> +    paste(anndir, "AraGene-1_0-st-v1.na33.tair10.transcript.csv",sep="/"))
>
> I get the following Error:
>
>   Error in import.exon.scheme("Scheme_AraGene10stv1_na32", filedir = scmdir,  :
>    error in function ‘ImportExonSchemes’
> Creating new file </Users/Endo/desktop/workspace/scmdir/Scheme_AraGene10stv1_na33.root>...
> Importing </Users/Endo/desktop/workspace/libdir/AraGene-1_0-st.clf> as <AraGene-1_0-st.cxy>...
>     <610001> recError: Premature end of file <~/desktop/workspace/anndir/AraGene-1_0-st-v1.na33.tair10.probeset.csv> reached.
> Error: Missing probeset annotation tree <AraGene-1_0-st.anp>.
> Error: Could not get tree <~/desktop/workspace/libdir/AraGene-1_0-st.pgf>.
>     <1416100> records imported...Finishedworkspace/anndir/AraGene-1_0-st-v1.na33.tair10.probeset.csv> reached.
> New dataset <AraGene-1_0-st> is added to Content...
> Importing </Users/Endo/desktop/workspace/anndir/AraGene-1_0-st-v1.na33.tair10.probeset.csv> as <AraGene-1_0-st.anp>...
> Importing </Users/Endo/desktop/workspace/libdir/AraGene-1_0-st.pgf> as <AraGene-1_0-st.scm>...
>
> and then get stuck.
> What's going on?
> Any help would be very appreciated
>
> Many thanks,
>
> Endo Motomu
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] ja_JP.UTF-8/ja_JP.UTF-8/ja_JP.UTF-8/C/ja_JP.UTF-8/ja_JP.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xps_1.18.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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