[BioC] Affymetrix Promoter tiling array

[Ben Bolstad]

You need a newer version of affyio. This bug has been fixed.

Best,

Ben




On Wed, 2006-08-30 at 15:06 -0700, Wu, Xiwei wrote:
> Hi, Benilton,
> 
> Thank you so much for your help. I downloaded both packages and installed into R-2.3.1 under Redhat Linux WS v3. When I try to build the promoter tiling array package, I got the following error:
> 
> 
> > makePDpackage("Hs_PromPF_v02-3_NCBIv34.bpmap", file1="Hs_PromPF_v02.cif", manufacturer="affymetrix", type="tiling")
> affymetrix tiling
> The package will be called pdhsprompfv023ncbiv34
> Error in makeBPMAPenv(designFile, genomebuild = genomebuild) :
>         'names' attribute [9] must be the same length as the vector [7]
> > traceback()
> 3: .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE = "affyio")
> 2: makeBPMAPenv(designFile, genomebuild = genomebuild)
> 1: makePDpackage("Hs35b_P07R_v01-3_NCBIv34.bpmap", file1 = "Hs35b_P07R_v01.cif",
>        manufacturer = "affymetrix", type = "tiling", genomebuild = "hg14")
> 
> > sessionInfo()
> Version 2.3.0 (2006-04-24)
> x86_64-unknown-linux-gnu
>  
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
>  
> other attached packages:
>            session              oligo            Biobase makePlatformDesign
>            "1.0.1"          "0.99.17"           "1.10.0"          "0.99.16"
>             affyio
>            "1.0.0"
> 
> 
> Any suggestions?
> 
> Xiwei
> 
> -----Original Message-----
> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
> Sent: Fri 8/11/2006 1:18 PM
> To: Wu, Xiwei
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Affymetrix Promoter tiling array
>  
> The oligo and makePlatformDesign packages can handle those...
> 
> the latest (devel) version was just committed to the bioc servers and  
> may take a while to become available...
> 
> meanwhile you can download from:
> 
> http://www.biostat.jhsph.edu/~bcarvalh/research.html
> 
> you'll also need to CIF files to build the environments for affy  
> tiling arrays..
> 
> let me know how it goes,
> 
> b.
> 
> On Aug 11, 2006, at 3:40 PM, Wu, Xiwei wrote:
> 
> > Hi, all,
> >
> > I was given some CHIP-on-chip data using Affymetrix promoter tiling
> > array. I looked through the board and could not find any  
> > information on
> > this chip type.
> >
> > It seems to me that the CEL files have different number of features  
> > from
> > the BPMAP file. Does anyone have a CDF created for this chip type? I
> > can't get makecdfenv working with the BPMAP file downloaded from
> > Affymetrix.
> >
> > Any help will be appreciated.
> >
> > Xiwei Wu
> >
> > "EMF <COH.ORG>" made the following annotations.
> > ---------------------------------------------------------------------- 
> > --------
> > SECURITY/CONFIDENTIALITY WARNING:  This message and any atta... 
> > {{dropped}}
> >
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> 
> 
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