[BioC] probeAnno for tilingArray package.

[Wolfgang Huber]

On Sep/14/10 7:36 PM, sohkhan at notes.cc.sunysb.edu wrote:
> Thank you Wolfgang.
> I corrected the chr parameter as suggested by Noah. segChrom runs with
> strand=NA. Now, I have question about the probeAnno creation by
> bpmapToProbeAnno(). Does the function treat 0's as "-" and 1's "+" strand.
> I have just one BPMAP file for S.pombe from Affymetrix which contains
> 0's and 1's in the strand column.

Why don't you just try and report problems, if any?

       Wolfgang

> Thanks again.
> -Sohail
>
>
>
> From: Wolfgang Huber <whuber at embl.de>
> To: bioconductor at stat.math.ethz.ch
> Date: 09/11/2010 08:15 AM
> Subject: Re: [BioC] probeAnno for tilingArray package.
> Sent by: bioconductor-bounces at stat.math.ethz.ch
> ------------------------------------------------------------------------
>
>
>
> 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
>  >>
>  > [[alternative HTML version deleted]]
>  >
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> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
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-- 


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