[BioC] Affymetrix Promoter tiling array

[Benilton Carvalho]

Hi Xiwei,

could you please send us the output from

traceback()

executed right after when you get the error?

(is this an installation you'd be willing to update Biobase to  
1.11.30 and give it a try after that? note that it's not recommended  
to mix stable and devel releases)

b

On Aug 30, 2006, at 7:35 PM, Wu, Xiwei wrote:

> Thanks a lot, Ben. I updated the affyio package to v1.1.8, and now  
> I am getting another error message:
>
> > 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 .subset2(x, i) : subscript out of bounds
> In addition: Warning message:
> longer object length
>         is not a multiple of shorter object length in: clabs == nmi
>
>
>
>
>
> -----Original Message-----
> From: Ben Bolstad [mailto:bmb at bmbolstad.com]
> Sent: Wed 8/30/2006 3:26 PM
> To: Wu, Xiwei
> Cc: Benilton Carvalho; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Affymetrix Promoter tiling array
>
> 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.
> > >  
> ----------------------------------------------------------------------
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