And for making custom annotations (so you can get GO terms etc.) you should be able to use the SQLForge code in AnnotationDbi: http://www.bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html Marc Mark Robinson wrote: > Edward. > > 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. > > Cheers, > Mark > > > On 01/12/2008, at 5:51 PM, Edward Oakeley wrote: > >> 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 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > ------------------------------ > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >