[BioC] XPS with Arabidopsis Gene 1.1 ST Array Strip

[cstrato]

Dear Benedikt,

I have just downloaded from Affymetrix strip array data for the 
HuGene-1_1_st array and can confirm your error messages. This means that 
xps does currently only support plate array data but does not support 
strip array data for the same type of expression array.

Best regards,
Christian


On 7/9/14 8:19 PM, cstrato wrote:
> 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
> _._._._._._._._._._._._._._._._._._
>
>
>
>
> 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.
>>
>
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