[BioC] probeAnno for tilingArray package.
Wolfgang Huber
whuber at embl.de
Wed Sep 15 15:25:50 CEST 2010
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
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