[BioC] probeAnno for tilingArray package.

[Wolfgang Huber]

Dear Sohail

in R, the character string "NA" is different from the value NA. Try with 
supplying the second one for the argument 'strands'. Also, please make 
sure that the 'chr' argument is set to the right value, the default 
(1:17) is likely not to work with S.pombe. You can see what the 
chromosome names are in your organism by inspecting the probeAnno object.

Best wishes
	Wolfgang

On Sep/8/10 10:33 PM, sohkhan at notes.cc.sunysb.edu wrote:
> Hi all,
>
> I am trying to use the "tilingArray" package to analyze Affymetrix S.pombe
> tiling arrays.  I downloaded the .bpmap file from Affymetrix's website,
> and created a probeAnno object by bpmapToProbeAnno().
> However, I am getting the following error when I try to segment the data
> by segChrom().
>
>> segdf<-segChrom(cels,probeAnno,strands="NA")
> Running 'segment' on chromosome 1.NAError in probeAnno[w] :
>    No mapping '1.NA.start' in this 'probeAnno' object.
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>   [1] davidTiling_1.2.12   GO.db_2.4.1          RSQLite_0.9-2 DBI_0.2-5
> AnnotationDbi_1.10.2 tilingArray_1.26.0   pixmap_0.4-10        Starr_1.4.4
>
>   [9] affy_1.26.1          Ringo_1.12.0         Matrix_0.999375-39
> lattice_0.18-8       limma_3.4.4          RColorBrewer_1.0-2 Biobase_2.8.0
>         affxparser_1.20.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.16.0         annotate_1.26.1       genefilter_1.30.0
> MASS_7.3-6            preprocessCore_1.10.0 pspline_1.0-14 splines_2.11.1
>       strucchange_1.4-1
>   [9] survival_2.35-8       tools_2.11.1          vsn_3.16.0 xtable_1.5-6
>
>
> I am wondering if I used the correct .bpmap file??
> Thanks for any suggestion/advice.
>
> -Sohail
> SBU, NY
>>
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>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber