[BioC] Custom CDF files
mcarlson at fhcrc.org
Mon Dec 1 18:33:50 CET 2008
And for making custom annotations (so you can get GO terms etc.) you
should be able to use the SQLForge code in AnnotationDbi:
Mark Robinson wrote:
> Given that you have a CDF file (or can make one easily) and you want
> RMA-summarized values, I suggest you try one of:
> 1. use 'make.cdf.package' in the makecdfenv package to take the CDF
> file and create the annotation package ... then install the package
> with an 'R CMD INSTALL' ... then on with 'rma'.
> 2. use aroma.affymetrix -- CDF file goes in 1 directory, CEL files go
> in another, and you're set ... then on with your summaries.
> On 01/12/2008, at 5:51 PM, Edward Oakeley wrote:
>> 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
>> 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?
>> 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
>>> bpmapFile <- "Hs35b_P06R_v01-3_NCBIv36.bpmap"
>>> cifFile <- "Hs35b_P06R_v01.cif"
>>> obj <- new("AffyTilingPDInfoPkgSeed",
>>> author="Benilton Carvalho",
>>> email="bcarvalh at jhsph.edu",
>>> genomebuild="NCBI Build 36",
>>> makePdInfoPackage(obj, destDir=".")
>>> 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.
>>>> works fine with applications that can accept CDF files but I would
>>>> to use Bioconductor to condense expression values. It would also be
>>>> 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
>>>> if some scripts exist for automating this process.
>>>> Any ideas?
>>>> Edward Oakeley
>>>> FMI, Basel
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> Search the archives:
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives:
> Mark Robinson
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robinson at garvan.org.au
> e: mrobinson at wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives:
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