[BioC] XPS with Arabidopsis Gene 1.1 ST Array Strip

[cstrato]

Dear Benedikt,

In principle, xps should support this array.

Can you show me how you have created the scheme file 'scheme.Ara'? The 
code should be something like:

scheme.aragene11st <- import.exon.scheme("aragene11st", filedir = 
file.path(scmdir, "na34"),
file.path(libdir, "AraGene-1_1-st.clf"),
file.path(libdir, "AraGene-1_1-st.pgf"),
file.path(anndir, "Version14May", 
"AraGene-1_1-st-v1.na34.tair10.probeset.csv"),
file.path(anndir, "Version14May", 
"AraGene-1_1-st-v1.na34.tair10.transcript.csv"))

The error messages indicate that the CEL-files do not belong to the 
scheme or that they are in an unknown format.

The GEO profile number for the Affymetrix AraGene-1_1-st array seems to 
be GPL17133. Sadly, there does not exist any data samples so that I 
cannot test this array. Thus could you please send me some CEL-files for 
this array so that I can test it.

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
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On 7/9/14 4:30 PM, Benedikt [guest] wrote:
> Hi,
>
> I would like to analyse data from the Arabidopsis Gene 1.1 ST Array Strip with the XPS package. I created a scheme and tried to load some example data with with the function import.data(). This error message will appear:
>
> -------------------------
> dataAll <- import.data(scheme.Ara, "AraGene1_1", celdir=celdir, celfiles=celfiles)
> Opening file </home/bathmer/R_projekte/monika/xps_test/libraryfiles/schemes/Scheme_Ara11ST_NA34.root> in <READ> mode...
> Creating new file </home/bathmer/R_projekte/monika/xps_test/AraGene1_1_cel.root>...
> Importing </home/bathmer/R_projekte/monika/xps_test/cel/AraGene-1_1-st_hybridization-rep_strip-1_A01.cel> as <AraGene_1_1_st_hybridization_rep_strip_1_A01.cel>...
> Error: Number of data groups is not 1!
> Error: CEL-file with version/magic number </home/bathmer/R_projekte/monika/xps_test/cel/AraGene-1_1-st_hybridization-rep_strip-1_A01.cel> is not supported.
> Fehler in import.data(scheme.Ara, "AraGene1_1", celdir = celdir, celfiles = celfiles) :
>    error in function ‘ImportData’
> Zusätzlich: Warnmeldung:
> In import.data(scheme.Ara, "AraGene1_1", celdir = celdir, celfiles = celfiles) :
>    characters [](){}.:# etc in 'celnames' will be replaced  with '_'
> ----------------------------
>
> Does XPS support this kind of cel files?
>
> Regards,
>
> Benedikt
>
>   -- output of sessionInfo():
>
> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=de_DE.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=de_DE.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xps_1.24.0
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.2
>> traceback()
> Kein traceback vefügbar
>
> --
> Sent via the guest posting facility at bioconductor.org.
>