[BioC] Custom CDF files

[Edward Oakeley]

Hi,

Sorry for not being clear. The Affymetrix BPMAP file is not much use as
a format for me because we mostly use S.pombe tiling arrays. Three
problems with the pombe array: 1) it has oligos that alternate in their
strand orientation (so it goes +,-,+,-,...) but the strand info is not
encoded in the BPMAP file so you have to align it to the genome; 2) Affy
only make a BPMAP file against an ancient sequence assembly for which
the annotations are very very poor; 3) Only the Sanger have the
annotations on their website (not the NCBI/UCSC) and these must be
downloaded as GFF files.

Given 1-3 and the fact that I need to make RMA expression values for the
gene regions the simplest approach is to make CDF files which is
actually a trivial task as the CDF format for genomic intervals is very
straightforward.

Given that someone somewhere is able to make packages for Bioconductor
for expression arrays (which is what we now have in effect) I was just
wondering if anyone knew how this can be done. I can condense them in
RMAexpress but it would be nice to make a simple workflow that can be
used by anyone working with these chips (i.e. make a CDF package and add
all the Sanger annotations to it).

Can anyone help?

Thanks
Edward


On Mon, 2008-12-01 at 01:18 -0200, Benilton Carvalho wrote:
> For tiling arrays, Affymetrix provides BPMAP files. You can use the  
> pdInfoBuilder package to create an annotation package. Once the  
> annotation package is installed, you can use the oligo package to read  
> the data in.
> 
> For example, with pdInfoBuilder, you can use something like the  
> following:
> 
> library(pdInfoBuilder)
> bpmapFile <- "Hs35b_P06R_v01-3_NCBIv36.bpmap"
> cifFile <- "Hs35b_P06R_v01.cif"
> obj <- new("AffyTilingPDInfoPkgSeed",
>             version="0.1",
>             author="Benilton Carvalho",
>             email="bcarvalh at jhsph.edu",
>             biocViews="AnnotationData",
>             genomebuild="NCBI Build 36",
>             bpmapFile=bpmapFile,
>             cifFile=cifFile)
> makePdInfoPackage(obj, destDir=".")
> 
> 
> best,
> 
> b
> 
> On Nov 30, 2008, at 7:07 PM, Edward Oakeley wrote:
> 
> > Hi there,
> >
> > I make custom CDF files for use with our Affy tiling arrays. Each  
> > one I
> > make by aligning the oligos to the latest genome build and then
> > intersecting the coordinates with the latest GFF annotation files.  
> > This
> > works fine with applications that can accept CDF files but I would  
> > like
> > to use Bioconductor to condense expression values. It would also be  
> > nice
> > if there was an easy way to link in things like GO terms etc that are
> > usually available from the genome repositories.
> >
> > Could you tell me how the CDF repositories are made for Bioconductor  
> > and
> > if some scripts exist for automating this process.
> >
> > Any ideas?
> >
> > Thanks
> >
> > Edward Oakeley
> > FMI, Basel
> >
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