Hi, I was a little curious to know what these scripts are able to construct/convert, so I had a quick look at the codes. @ Elizabeth (or others): Although I am not planning to use these (yet), there is one thing that (naively?) did not become immediately clear to me: what is the expected content of the file "annotExonBoundaries" that is required for the (1st) function "annotateProbesets.R", (and how would generate such file)?
>From the description in the script: exonBoundariesFile=file name of deliminated file with the exon boundaries that you want to map the probesets to. ##annotExonBoundaries<-file.path(outdir,"exonBoundaries_proteinCoding_20080819.txt") Thanks, Guido --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiv...@wur.nl internet: http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson Sent: Wednesday, January 22, 2014 21:15 To: aroma-affymetrix@googlegroups.com Subject: Re: [aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file Alright, so Elizabeth Purdom found the missing files and kindly sent them to me. I've now uploaded them the http://aroma-project.org server and updated the links on http://aroma-project.org/node/40 accordingly. Hope this helps Henrik On Tue, Jan 21, 2014 at 3:35 PM, Henrik Bengtsson <henrik.bengts...@aroma-project.org> wrote: > Hi, > > thanks for reporting on this. > > On Mon, Jan 20, 2014 at 2:09 PM, Guilherme Rocha <gvro...@gmail.com> wrote: >> Dear all, >> >> Does anybody know of any good tools for constructing a cdf file from >> affy pgf and clf files? >> >> It appears that such tools exist: >> http://www.aroma-project.org/node/40 >> >> The problem is the following 3 links in above address are broken: >> >> 1) http://bcgc.lbl.gov/cdfFiles/flat2Cdf.R >> Flat2cdf.R (constructs a cdf file from a "flat file") > > It turns out that that file is the same as > > http://bioinf.wehi.edu.au/folders/mrobinson/exon/flat2Cdf.R > > I've update the webpage to link to that instead (for now). > >> >> 2) http://bcgc.lbl.gov/cdfFiles/combineProbeInfo.pl >> combineProbeInfo.pl (combines pgf and clf files into single flat file >> with each row containing most of the information needed for each >> probe) > > Unfortunately, I cannot locate this elsewhere. > >> >> 3) http://bcgc.lbl.gov/cdfFiles/addGeneId.pl >> addGeneId.pl (takes output of previous pl script and merge it with >> probeset-gene map to generate flat file needed by flat2cdf) > > Unfortunately, same for this one (and the other links on that page). > > If you can generate a "flat" text-files as on illustrated on that > page, you could still create a CDF. However, note that the flat2Cdf() > function is rather specific to gene-exon chip types, so if you're > looking to create other types of CDF files, it won't work (at least > not out of the box). > > I've updated http://aroma-project.org/node/40 with the following note: > > Note: Several of the links to the external third party R and Perl > scripts are broken, i.e. annotateProbesets.R, > convertProbesetCSV_differentInput.pl, selectProbes.pl > combineProbeInfo.pl, addGeneId.pl. If you have any of these files > sitting around, please consider sending them to use. Thanks /HB > 2014-01-20 > > Thanks, > > Henrik > >> >> Any help greatly appreciated. >> >> Thanks, >> >> Guilherme Rocha >> >> >> -- >> -- >> When reporting problems on aroma.affymetrix, make sure 1) to run the >> latest version of the package, 2) to report the output of >> sessionInfo() and traceback(), and 3) to post a complete code example. >> >> >> You received this message because you are subscribed to the Google >> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. >> To post to this group, send email to >> aroma-affymetrix@googlegroups.com To unsubscribe and other options, >> go to http://www.aroma-project.org/forum/ >> >> --- >> You received this message because you are subscribed to the Google >> Groups "aroma.affymetrix" group. >> To unsubscribe from this group and stop receiving emails from it, >> send an email to aroma-affymetrix+unsubscr...@googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. 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